Digital Commons Network^™

Selfie-Takers Prefer Left Cheeks: Converging Evidence From The (Extended) Selfiecity Database, Lev Manovich, Vera Ferrari, Nicola Bruno

Publications and Research

According to previous reports, selfie takers in widely different cultural contexts prefer poses showing the left cheek more than the right cheek. This posing bias may be interpreted as evidence for a right-hemispheric specialization for the expression of facial emotions. However, earlier studies analyzed selfie poses as categorized by human raters, which raises methodological issues in relation to the distinction between frontal and three-quarter poses. Here, we provide converging evidence by analyzing the (extended) selfiecity database which includes automatic assessments of head rotation and of emotional expression. We confirm a culture- and sex-independent left-cheek bias and report stronger expression of …

Bacterial Diversity Impacts As A Result Of Combined Sewer Overflow In A Polluted Waterway, Olga Calderón, Holly Porter-Morgan, Joby Jacob, Willis Elkins

Publications and Research

Newtown Creek is an industrial waterway and former tidal wetland in New York City. It is one of the most polluted water bodies in the United States and was designated as a superfund site in 2010. For over a century, organic compounds, heavy metals, and other forms of industrial pollution have disrupted the creek’s environment. The creek is also impacted by discharges from twenty combined sewer overflow pipes, which may deposit raw sewage or partially treated wastewater directly into the creek during heavy or sustained rain events. Combined sewer overflow events and associated nutrient over-enrichment at the creek drive eutrophication …

Design And Revision Of An Open-Educational Resource Microbiology Lab Manual Using Student Feedback, Joan Petersen, Susan K. Mclaughlin

Publications and Research

Open educational resources are becoming increasingly important in higher education, and are a valuable resource for instructors who want to customize course content while saving their students money. We designed, revised, and assessed an open educational resource for our Principles of Microbiology course. Student feedback was used to guide the revisions, which took place over the course of several semesters. Student survey responses to lab manual content were very positive, and students overwhelmingly favored a no-cost online manual over one that is commercially published. The process we used to develop this lab manual serves as an example for others who …

Studying The Mechanisms Of Developmental Vocal Learning And Adult Vocal Performance In Zebra Finches Through Lentiviral Injection, Zhimin Shi, Ofer Tchernichovski, Xiaoching Li

Publications and Research

Here we provide a detailed step-by-step protocol for using lentivirus to manipulate miRNA expression in Area X of juvenile zebra finches and for analyzing the consequences on song learning and song performance. This protocol has four parts: 1) making the lentiviral construct to overexpress miRNA miR-9; 2) packaging the lentiviral vector; 3) stereotaxic injection of the lentivirus into Area X of juvenile zebra finches; 4) analysis of song learning and song performance in juvenile and adult zebra finches. These methods complement the methods employed in recent works that showed changing FoxP2 gene expression in Area X with lentivirus or adeno-associated …

Engineered Aptamers To Probe Molecular Interactions On The Cell Surface, Sana Batool, Sanam Bhandari, Shanell George, Precious Okeoma, Nabeela Van, Hazan E. Zümrüt, Prabodhika Mallikaratchy

Publications and Research

Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in …

Climate Matching Drives Spread Rate But Not Establishment Success In Recent Unintentional Bird Introductions, Pedro Abellán, José L. Tella, Martina Carrete, Laura Cardador, José D. Anadón

Publications and Research

Understanding factors driving successful invasions is one of the cornerstones of invasion biology. Bird invasions have been frequently used as study models, and the foundation of current knowledge largely relies on species purposefully introduced during the 19th and early 20th centuries in countries colonized by Europeans. However, the profile of exotic bird species has changed radically in the last decades, as birds are now mostly introduced into the invasion process through unplanned releases from the worldwide pet and avicultural trade. Here we assessed the role of the three main drivers of invasion success (i.e., event-, species-, and location-level factors) on …

The Farnesoid X Receptor Negatively Regulates Osteoclastogenesis In Bone Remodeling And Pathological Bone Loss, Ting Zheng, Ju-Hee Kang, Jung-Sun Sim, Jung-Woo Kim, Jeong-Tae Koh, Chan Soo Shin, Hyungsik Lim, Mijung Yim

Publications and Research

Farnesoid X receptor (FXR, NR1H4) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. Since the role of FXR in osteoclast differentiation remains ill-defined, we investigated the biological function of FXR on osteoclastogenesis, using FXR-deficient mice. We demonstrated that FXR deficiency increases osteoclast formation in vitro and in vivo. First, FXR deficiency was found to accelerate osteoclast formation via down-regulation of c-Jun N-terminal kinase (JNK) 1/2 expression. Increased expression of peroxisome proliferator-activated receptor (PPAR)γ and peroxisome proliferator-activated receptor gamma coactivator 1 (PGC- 1)β seems to mediate the pro-osteoclastogenic effect of FXR deficiency via the JNK pathway. In …

Funding Science With Science: Cryptocurrency And Independent Academic Research Funding, Edward Lehner, Dylan Hunzeker, John R. Ziegler

Publications and Research

Scientific funding within the academy is an often complicated affair involving disparate and competing interests. Private universities, for instance, are vastly outpacing public institutions in garnering large, prestigious grants. Inequities also extend to the kinds of research funded, with government, corporate, and even military interests privileging certain types of inquiry. This work proposes an innovative type of research fund using cryptocurrencies, a fast-growing asset class. Although not a total funding solution, staking coins, specifically, can be strategically invested in to yield compound interest. These coins use masternode technologies to collateralize the network and speed transaction pace. Additionally, these staking coins …

Strategies For Improving Approximate Bayesian Computation Tests For Synchronous Diversification, Isaac Overcast, Justin C. Bagley, Michael J. Hickerson

Publications and Research

Background: Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization.

Methods: Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice …

The Heat Shock Response And Humoral Immune Response Are Mutually Antagonistic In Honey Bees, Mia Mckinstry, Charlie Chung, Henry Truong, Brittany A. Johnston, Jonathan W. Snow

Publications and Research

The honey bee is of paramount importance to humans in both agricultural and ecological settings. Honey bee colonies have suffered from increased attrition in recent years, stemming from complex interacting stresses. Defining common cellular stress responses elicited by these stressors represents a key step in understanding potential synergies. The proteostasis network is a highly conserved network of cellular stress responses involved in maintaining the homeostasis of protein production and function. Here, we have characterized the Heat Shock Response (HSR), one branch of this network, and found that its core components are conserved. In addition, exposing bees to elevated temperatures normally …

Choline Supplementation Normalizes Fetal Adiposity And Reduces Lipogenic Gene Expression In A Mouse Model Of Maternal Obesity, Chauntelle Jack-Roberts, Yaelle Joselit, Khatia Nanobashvili, Rachel Bretter, Olga V. Malysheva, Marie A. Caudill, Anjana Saxena, Kathleen Axen, Ahmed Gomaa, Xinyin Jiang

Publications and Research

Maternal obesity increases fetal adiposity which may adversely affect metabolic health of the offspring. Choline regulates lipid metabolism and thus may influence adiposity. This study investigates the effect of maternal choline supplementation on fetal adiposity in a mouse model of maternal obesity. C57BL/6J mice were fed either a high-fat (HF) diet or a control (NF) diet and received either 25 mM choline supplemented (CS) or control untreated (CO) drinking water for 6 weeks before timed-mating and throughout gestation. At embryonic day 17.5, HF feeding led to higher (p < 0.05) percent total body fat in fetuses from the HFCO group, while the choline supplemented HFCS group did not show significant difference versus the NFCO group. Similarly, HF feeding led to higher (p < 0.05) hepatic triglyceride accumulation in the HFCO but not the HFCS fetuses. mRNA levels of lipogenic genes such as Acc1, Fads1, and Elovl5, as well as the transcription factor Srebp1c that favors lipogenesis were downregulated (p < 0.05) by maternal choline supplementation in the HFCS group, which may serve as a mechanism to reduce fat accumulation in the fetal liver during maternal HF feeding. In summary, maternal choline supplementation improves indices of fetal adiposity in obese dams at late gestation.

Thyroid Function And Ischemic Heart Disease: A Mendelian Randomization Study, Jie V. Zhao, C. Mary Schooling

Publications and Research

To clarify the role of thyroid function in ischemic heart disease (IHD) we assessed IHD risk and risk factors according to genetically predicted thyroid stimulating hormone (TSH), free thyroxine (FT4) and thyroid peroxidase antibody (TPOAb) positivity. Separate-sample instrumental variable analysis with genetic instruments (Mendelian randomization) was used in an extensively genotyped case (n = 64,374)-control (n = 130,681) study, CARDIoGRAMplusC4D. Associations with lipids, diabetes and adiposity were assessed using the Global Lipids Genetics Consortium Results (n = 196,475), the DIAbetes Genetics Replication And Meta-analysis case (n = 34,380)-control (n = 114,981) study, and the Genetic Investigation of ANthropometric Traits (body …

Inflammation And Bone Mineral Density: A Mendelian Randomization Study, Jian V. Huang, C. Mary Schooling

Publications and Research

Osteoporosis is a common age-related disorder leading to an increase in osteoporotic fractures and resulting in significant suffering and disability. Inflammation may contribute to osteoporosis, as it does to many other chronic diseases. We examined whether inflammation is etiologically relevant to osteoporosis, assessed from bone mineral density (BMD), as a new potential target of intervention, or whether it is a symptom/biomarker of osteoporosis. We obtained genetic predictors of inflammatory markers from genome-wide association studies and applied them to a large genome wide association study of BMD. Using two-sample Mendelian randomization, we obtained unconfounded estimates of the effect of high-sensitivity C-reactive …

Thermodynamic And Kinetic Analyses Of Iron Response Element (Ire)-Mrna Binding To Iron Regulatory Protein, Irp1, Mateen A. Khan, William E. Walden, Elizabeth C. Theil, Dixie J. Goss

Publications and Research

Comparison of kinetic and thermodynamic properties of IRP1 (iron regulatory protein1) binding to FRT (ferritin) and ACO2 (aconitase2) IRE-RNAs, with or without Mn2+, revealed differences specific to each IRE-RNA. Conserved among animal mRNAs, IRE-RNA structures are noncoding and bind Fe2+ to regulate biosynthesis rates of the encoded, iron homeostatic proteins. IRP1 protein binds IRERNA, inhibiting mRNA activity; Fe2+ decreases IRE-mRNA/IRP1 binding, increasing encoded protein synthesis. Here, we observed heat, 5 °C to 30 °C, increased IRP1 binding to IRE-RNA 4-fold (FRT IRE-RNA) or 3-fold (ACO2 IRE-RNA), which was enthalpy driven and entropy favorable. Mn2+ (50 μM, 25 °C) increased IRE-RNA/IRP1 …

Funding Science With Science (And, Admittedly, A Lot Of Math), John R. Ziegler, Dylan Hunzeker, Edward Lehner

Publications and Research

Scientific funding within the academy is an often complicated affair involving disparate and competing interests. Private universities, for instance, are vastly outpacing public institutions in garnering large, prestigious grants. Inequities also extend to the kinds of research funded, with government, corporate, and even military interests privileging certain types of inquiry.This work proposes an innovative type of research fund using cryptocurrencies, a fast growing asset class. Although not a total funding solution, staking coins, specifically, can be strategically invested in to yield compound interest. These coins use central hub technology to collateralise the network and speed transaction pace. Additionally. These staking …

Albright Uses Avatars, Horses To Improve Mental Health., Aldemaro Romero Jr.

Publications and Research

“When I was a college student, I was struggling in an intimate relationship I was forming, and it got to the point where I had to do something about it. So I went into the counseling center, and that’s what really turned me on—noticing the change within myself and the impact of counseling on the way we view our lives.”

That is the way Dr. Glenn Albright explains how he became interested in psychology in general and in counseling in particular. A native of Albany, New York, Albright received his bachelor’s in biology from Parson College in Iowa, his MS …

Sexual Dimorphism In Striatal Dopaminergic Responses Promotes Monogamy In Social Songbirds, Kirill Tokarev, Julia Hyland Bruno, Iva Ljubicic, Paresh J. Kothari, Santosh A. Helekar, Ofer Tchernichovski, Henning U. Voss

Publications and Research

In many songbird species, males sing to attract females and repel rivals. How can gregarious, non-territorial songbirds such as zebra finches, where females have access to numerous males, sustain monogamy? We found that the dopaminergic reward circuitry of zebra finches can simultaneously promote social cohesion and breeding boundaries. Surprisingly, in unmated males but not in females, striatal dopamine neurotransmission was elevated after hearing songs. Behaviorally too, unmated males but not females persistently exchanged mild punishments in return for songs. Song reinforcement diminished when dopamine receptors were blocked. In females, we observed song reinforcement exclusively to the mate’s song, although their …

Modeling And Visualizing Bacterial Colony Purification Without The Use Of Bacteria Or Laboratory Equipment, Grace L. Axler-Diperte

Publications and Research

This paper describes an activity that simulates bacterial purification without the use of biohazardous materials and provides immediate feedback to students regarding the efficacy of their technique.

Draft Nuclear Genome, Complete Chloroplast Genome, And Complete Mitochondrial Genome For The Biofuel/ Bioproduct Feedstock Species Scenedesmus Obliquus Strain Doe0152z, S. R. Starkenburg, Juergen Polle, B. Hovde, H. E. Daligault, K. W. Davenport, A. Huang, P. Neofotis, Zaid Mckie-Krisberg

Publications and Research

The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Glycomics For Microbes And Microbiologists, Peter N. Lipke

Publications and Research

The recent article “Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins” by Ielasi et al. describes a new development in microbial carbohydrate analysis [Ielasi FS, Alioscha-Perez M, Donohue D, Claes S, Sahli H, Schols D, Willaert RG, mBio 7(4):e00584-16, 2016, http://dx.doi.org/10.1128/mbio.00584-16]. Specific carbohydrate ligands have been identified from the patterns of lectin binding to oligosaccharides printed on a chip. The new technique links the output to a comprehensive glycan database and offers a number of data visualization options. The graphs highlight the occurrence of potential ligands, organized by organism, tissue, and patterns of association with disease states. …

Bow-Tie Signaling In C-Di-Gmp: Machine Learning In A Simple Biochemical Network, Jinyuan Yan, Maxime Deforet, Kerry E. Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E. P. Dietrich, Weigang Qiu, Joao B. Xavier

Publications and Research

Bacteria of many species rely on a simple molecule, the intracellular secondary messenger c-di-GMP (Bis-(3'-5')-cyclic dimeric guanosine monophosphate), to make a vital choice: whether to stay in one place and form a biofilm, or to leave it in search of better conditions. The c-di-GMP network has a bow-tie shaped architecture that integrates many signals from the outside worldÐthe input stimuliÐinto intracellular c-di-GMP levels that then regulate genes for biofilm formation or for swarming motilityÐthe output phenotypes. How does the `uninformed' process of evolution produce a network with the right input/output association and enable bacteria to make the right choice? Inspired …

On The Pursuit Of Relevance In Standards-Based Curriculum Development: The Ccny Approach, Angelo Lampousis

Publications and Research

The Society for Standards Professionals (SES) has a significant history of documenting the use of standards in research and academia. For instance, during the 62nd Annual SES Conference in 2013 in Savannah, Georgia, the author participated in such a session highlighting examples of relationships between academic institutions, government, and standards developing organizations. In this article, we attempt to capture the current advances made from similar relationships specific to our home institution, the City College of New York (CCNY) of the City University of New York (CUNY.) These advances have become possible through a grant issued under the Standards Services Curricula …

Retrotransposons Are The Major Contributors To The Expansion Of The Drosophila Ananassae Muller F Element, Wilson Leung, Gerard Mcneil

Publications and Research

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (.18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors …

The Influence Of The Electrode Dimension On The Detection Sensitivity Of Electric Cell–Substrate Impedance Sensing (Ecis) And Its Mathematical Modeling, Xudong Zhang, William Wang, Anis Nurashikin Nordin, Fang Li, Sunghoon Jang, Ioana Voiculescu

Publications and Research

Detection sensitivity is a crucial criterion in the design and application of ECIS sensors. The influence of sensing electrode dimension on detection sensitivity is investigated in this paper. Eight types of ECIS sensors were fabricated, and their experimental results reveal that smaller-radius working electrodes generate more sensitive impedance shift to cell density change. Also, the smaller radius of working electrodes yield higher impedance values, which improves signal-to-noise ratio. In a range from 1.0 mm to 3.5 mm, the distance between the working and counter electrodes does not affect impedance measurements. However, the distance should be large enough to prevent the …

Regulating Anger Under Stress Via Cognitive Reappraisal And Sadness, Jun Zhan, Xiaofei Wu, Jin Fan, Jiayou Guo, Jianshe Zhou, Jun Ren, Chang Liu, Jing Luo

Publications and Research

Previous studies have reported the failure of cognitive emotion regulation (CER), especially in regulating unpleasant emotions under stress. The underlying reason for this failure was the application of CER depends heavily on the executive function of the prefrontal cortex (PFC), but this function can be impaired by stress-related neuroendocrine hormones. This observation highlights the necessity of developing selfregulatory strategies that require less top-down cognitive control. Based on traditional Chinese philosophy and medicine, which examine how different types of emotions promote or counteract one another, we have developed a novel emotion regulation strategy whereby one emotion is used to alter another. …

Pulling The Plug On Microscopes In The Anatomy And Physiology Laboratory, Zvi Ostrin, Vyacheslav Dushenkov

Publications and Research

Virtual microscopy (VM) has been widely available for more than a decade, especially in clinical settings and medical schools. In recent years the movement away from conventional optical microscopy (OM) and towards VM has been accelerating and several VM websites are now available online and readily accessible to educators. VM can enhance the instructor’s ability to teach the histology component of anatomy and physiology classes, facilitate student learning, save time for both students and instructors, and ultimately save money that can be more productively used for other facets of the laboratory. The many pedagogical and practical advantages provided by VM …

Large-Scale Differences In Microbial Biodiversity Discovery Between 16s Amplicon And Shotgun Sequencing, Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M. Velgo, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael Lemke, Rob Desalle, Christopher E. Mason, Mercer R. Brugler

Publications and Research

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles …

Comparison Of The Long-Term Effect Of Positioning The Cathode In Tdcs In Tinnitus Patients, Sarah Rabau, Giriraj S. Shekhawat, Mohamed Aboseria, Daniel Griepp, Vincent Van Rompaey, Marom Bikson, Paul Van De Heyning

Publications and Research

Objective: Transcranial direct current stimulation (tDCS) is one of the methods described in the literature to decrease the perceived loudness and distress caused by tinnitus. However, the main effect is not clear and the number of responders to the treatment is variable. The objective of the present study was to investigate the effect of the placement of the cathode on the outcome measurements.

Methods: Patients considered for the trial were chronic non-pulsatile tinnitus patients with complaints for more than 3 months and a Tinnitus Functional Index (TFI) score that exceeded 25. The anode was placed on the right …

Dress And Sex: A Review Of Empirical Research Involving Human Participants And Published In Refereed Journals, Sharron J. Lennon, Alyssa Dana Adomaitis, Jayoung Koo, Kim K. P. Johnson

Publications and Research

Our research purpose was to assess research addressing relationships between dress and sex. Our review was focused on a 25 years span (i.e., 1990–2015) and on empirical research utilizing human participants published in refereed journals. Three main areas of research emerged: (1) dress used as cue to sexual information, (2) dress and sexual violence, and (3) dress, sex, and objectification. Our analyses revealed parents do invest their young children with sex-typed dress however sometimes children demand to wear such dress. Some women intentionally use dress to communicate sexual information but inferences about women who wear sexy dress can be misinterpreted …

T-Dna-Genome Junctions Form Early After Infection And Are Influenced By The Chromatin State Of The Host Genome, Shay Shilo, Pooja Tripathi, Cathy Melamed Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy

Publications and Research

Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of previously isolated sites of T-DNA integration in …