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During Natural Viewing, Neural Processing Of Visual Targets Continues Throughout Saccades, Atanas D. Stankov, Jonathan Touryan, Stephen Gordon, Anthony J. Ries, Jason Ki, Lucas C. Parra
During Natural Viewing, Neural Processing Of Visual Targets Continues Throughout Saccades, Atanas D. Stankov, Jonathan Touryan, Stephen Gordon, Anthony J. Ries, Jason Ki, Lucas C. Parra
Publications and Research
Relatively little is known about visual processing during free-viewing visual search in realistic dynamic environments. Free-viewing is characterized by frequent saccades. During saccades, visual processing is thought to be suppressed, yet we know that the presaccadic visual content can modulate postsaccadic processing. To better understand these processes in a realistic setting, we study here saccades and neural responses elicited by the appearance of visual targets in a realistic virtual environment. While subjects were being driven through a 3D virtual town, they were asked to discriminate between targets that appear on the road. Using a system identification approach, we separated overlapping …
The Naked Truth: A Comprehensive Clarification And Classification Of Current ‘Myths’ In Naked Mole‐Rat Biology, Rochelle Buffenstein, Vincent Amoroso, Blazej Andziak, Stanislav Avdieiev, Jorge Azpurua, Alison J. Barker, Nigel C. Bennett, Miguel A. Brieño‐Enríquez, Gary N. Bronner, Clive Coen, Martha A. Delaney, Christine M. Dengler‐Crish, Yael H. Edrey, Chris G. Faulkes, Daniel Frankel, Gerard Friedlander, Patrick A. Gibney, Vera Gorbunova, Christopher Hine, Melissa M. Holmes, Jennifer U. M. Jarvis, Yoshimi Kawamura, Nobuyuki Kutsukake, Cynthia Kenyon, Walid T. Khaled, Takefumi Kikusui, Joseph Kissil, Samantha Lagestee, John Larson, Amanda Lauer, Leonid A. Lavrenchenko, Angela Lee, Jonathan B. Levitt, Gary R. Lewin, Kaitlyn N. Lewis Hardell, Tzuhua D. Lin, Matthew J. Mason, Dan Mccloskey, Mary Mcmahon, Kyoko Miura, Kazutaka Mogi, Vikram Narayan, Timothy P. O'Connor, Kazuo Okanoya, M. Justin O'Riain, Thomas J. Park, Ned J. Place, Katie Podshivalova, Matthew E. Pamenter, Sonja J. Pyott, Jane Reznick, J. Graham Ruby, Adam B. Salmon, Joseph Santos‐Sacchi, Diana K. Sarko, Andrei Seluanov, Alyssa Shepard, Megan Smith, Kenneth B. Storey, Xiao Tian, Emily N. Vice, Mélanie Viltard, Akiyuki Watarai, Ewa Wywial, Masanori Yamakawa, Elena D. Zemlemerova, Michael Zions, Ewan St. John Smith
The Naked Truth: A Comprehensive Clarification And Classification Of Current ‘Myths’ In Naked Mole‐Rat Biology, Rochelle Buffenstein, Vincent Amoroso, Blazej Andziak, Stanislav Avdieiev, Jorge Azpurua, Alison J. Barker, Nigel C. Bennett, Miguel A. Brieño‐Enríquez, Gary N. Bronner, Clive Coen, Martha A. Delaney, Christine M. Dengler‐Crish, Yael H. Edrey, Chris G. Faulkes, Daniel Frankel, Gerard Friedlander, Patrick A. Gibney, Vera Gorbunova, Christopher Hine, Melissa M. Holmes, Jennifer U. M. Jarvis, Yoshimi Kawamura, Nobuyuki Kutsukake, Cynthia Kenyon, Walid T. Khaled, Takefumi Kikusui, Joseph Kissil, Samantha Lagestee, John Larson, Amanda Lauer, Leonid A. Lavrenchenko, Angela Lee, Jonathan B. Levitt, Gary R. Lewin, Kaitlyn N. Lewis Hardell, Tzuhua D. Lin, Matthew J. Mason, Dan Mccloskey, Mary Mcmahon, Kyoko Miura, Kazutaka Mogi, Vikram Narayan, Timothy P. O'Connor, Kazuo Okanoya, M. Justin O'Riain, Thomas J. Park, Ned J. Place, Katie Podshivalova, Matthew E. Pamenter, Sonja J. Pyott, Jane Reznick, J. Graham Ruby, Adam B. Salmon, Joseph Santos‐Sacchi, Diana K. Sarko, Andrei Seluanov, Alyssa Shepard, Megan Smith, Kenneth B. Storey, Xiao Tian, Emily N. Vice, Mélanie Viltard, Akiyuki Watarai, Ewa Wywial, Masanori Yamakawa, Elena D. Zemlemerova, Michael Zions, Ewan St. John Smith
Publications and Research
The naked mole‐rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled ‘Surprisingly long survival of premature conclusions about naked mole‐rat biology’ described 28 ‘myths’ which, those authors claimed, are a ‘perpetuation of beautiful, but falsified, hypotheses’ and impede our understanding of this enigmatic mammal. Here, we re‐examine each of …
Aurora Kinase A Inhibition Reverses The Warburg Effect And Elicits Unique Metabolic Vulnerabilities In Glioblastoma, Trang T. T. Nguyen, Enyuan Shang, Chang Shu, Sungsoo Kim, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Hee Won Yang, Hasan Orhan Akman, Catarina M. Quinzii, Guoan Zhang, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N. Bruce, Peter Canoll, Markus D. Siegelin
Aurora Kinase A Inhibition Reverses The Warburg Effect And Elicits Unique Metabolic Vulnerabilities In Glioblastoma, Trang T. T. Nguyen, Enyuan Shang, Chang Shu, Sungsoo Kim, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Hee Won Yang, Hasan Orhan Akman, Catarina M. Quinzii, Guoan Zhang, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N. Bruce, Peter Canoll, Markus D. Siegelin
Publications and Research
Aurora kinase A (AURKA) has emerged as a drug target for glioblastoma (GBM). However, resistance to therapy remains a critical issue. By integration of transcriptome, chromatin immunoprecipitation sequencing (CHIP-seq), Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq), proteomic and metabolite screening followed by carbon tracing and extracellular flux analyses we show that genetic and pharmacological AURKA inhibition elicits metabolic reprogramming mediated by inhibition of MYC targets and concomitant activation of Peroxisome Proliferator Activated Receptor Alpha (PPARA) signaling. While glycolysis is suppressed by AURKA inhibition, we note an increase in the oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO), which was …
Foundations Of Linguistics And Identity In L2 Teaching And Learning: Agency Through Linguistic Enrichment, Differentiated Instruction And Teacher Identity, Marnie Jo Petray, Rebecca Shapiro, Gladys M. Vega
Foundations Of Linguistics And Identity In L2 Teaching And Learning: Agency Through Linguistic Enrichment, Differentiated Instruction And Teacher Identity, Marnie Jo Petray, Rebecca Shapiro, Gladys M. Vega
Publications and Research
Language, procedure, and identity are L2 teaching/learning essentials that may promote agency and stimulate synergies among knowledge, practice, and reflection (Diaz Maggioli, 2014; Duff, 2012). This meta-report presents three studies that collectively advance agency and endorse linguistic foundations as enrichment, differentiated instruction as engagement, and teacher identity as empowerment. All of these theoretical constructs are key to successful L2 teaching and acquisition. Study 1 quantitatively reports on introductory linguistics’ presence or absence in 114 master’s programs at 54 US institutions. Findings suggest that linguistics’ curricular presence is inconsistent and training for optimal impact in the L2 classroom is lacking. Given …
Must Consent Be Informed? Patient Rights, State Authority, And The Moral Basis Of The Physician's Duties Of Disclosure, D. Robert Macdougall
Must Consent Be Informed? Patient Rights, State Authority, And The Moral Basis Of The Physician's Duties Of Disclosure, D. Robert Macdougall
Publications and Research
Legal standards of disclosure in a variety of jurisdictions require physicians to inform patients about the likely consequences of treatment, as a condition for obtaining the patient’s consent. Such a duty to inform is special insofar as extensive disclosure of risks and potential benefits is not usually a condition for obtaining consent in non-medical transactions.
What could morally justify the physician’s special legal duty to inform? I argue that existing justifications have tried but failed to ground such special duties directly in basic and general rights, such as autonomy rights. As an alternative to such direct justifications, I develop an …
The City As A Learning Lab: Using Historical Maps And Walking Seminars To Anchor Place-Based Research, Anne E. Leonard, Jason Montgomery
The City As A Learning Lab: Using Historical Maps And Walking Seminars To Anchor Place-Based Research, Anne E. Leonard, Jason Montgomery
Publications and Research
Information literacy, inquiry, and empirical observation skills are essential to undergraduate students’ success, supporting the development of their independent critical thinking skills. In this chapter, we discuss an interdisciplinary course that we, an architecture professor and a librarian, co-taught at New York City College of Technology. The course, Learning Places: Understanding the City, combines place-based learning with primary source research, developing students’ abilities to observe an urban site chosen for study and to document their observations, and in the process build a line of inquiry for further research. The documented observations, newly created primary sources in their own right, initiated …
No Ordinary Proteins: Adsorption And Molecular Orientation Of Monoclonal Antibodies, Ankit D. Kanthe, Andrew Ilott, Mary Krause, Songyan Zheng, Jinjiang Li, Wei Bu, Mrinal K. Bera, Binhua Lin, Charles Maldarelli, Raymond S. Tu
No Ordinary Proteins: Adsorption And Molecular Orientation Of Monoclonal Antibodies, Ankit D. Kanthe, Andrew Ilott, Mary Krause, Songyan Zheng, Jinjiang Li, Wei Bu, Mrinal K. Bera, Binhua Lin, Charles Maldarelli, Raymond S. Tu
Publications and Research
The interaction of monoclonal antibodies (mAbs) with air/water interfaces plays a crucial role in their overall stability in solution. We aim to understand this behavior using pendant bubble measurements to track the dynamic tension reduction and x-ray reflectivity to obtain the electron density profiles (EDPs) at the surface. Native immunoglobulin G mAb is a rigid molecule with a flat, “Y” shape, and simulated EDPs are obtained by rotating a homology construct at the surface. Comparing simulations with experimental EDPs, we obtain surface orientation probability maps showing mAbs transition from flat-on Y-shape configurations to side-on or end-on configurations with increasing concentration. …
Covid‑19, Race/Ethnicity, And Age: The Role Of Telemedicine To Close The Gaps On Health Disparities, Andreas Kakolyris, Juan J. Delacruz, Christos I. Giannikos
Covid‑19, Race/Ethnicity, And Age: The Role Of Telemedicine To Close The Gaps On Health Disparities, Andreas Kakolyris, Juan J. Delacruz, Christos I. Giannikos
Publications and Research
The novel COVID-19 outbreak is a major public health challenge that quickly turned into an economic recession of great proportions. This pandemic poses a trade-off between health and the economy where social distancing, quarantines, and isolation shut down demand and supply chains across the USA. This paper analyzes the impact of COVID-19 on illness and death among older adults and communities of color with low socioeconomic status in New York City. To achieve this goal, fractional logit models are used to capture changes in the novel virus’ morbidity and mortality rates at the neighborhood level. Median income, race/ethnicity, age, household …
Modeling Covid-19 Spread In Small Colleges, Riti Bahl, Nicole Eikmeier, Alexandra Fraser, Matthew Junge, Felicia Keesing, Kukai Nakahata, Lily Reeves
Modeling Covid-19 Spread In Small Colleges, Riti Bahl, Nicole Eikmeier, Alexandra Fraser, Matthew Junge, Felicia Keesing, Kukai Nakahata, Lily Reeves
Publications and Research
We develop an agent-based model on a network meant to capture features unique to COVID-19 spread through a small residential college. We find that a safe reopening requires strong policy from administrators combined with cautious behavior from students. Strong policy includes weekly screening tests with quick turnaround and halving the campus population. Cautious behavior from students means wearing facemasks, socializing less, and showing up for COVID-19 testing. We also find that comprehensive testing and facemasks are the most effective single interventions, building closures can lead to infection spikes in other areas depending on student behavior, and faster return of test …
Threshold Concentration And Random Collision Determine The Growth Of The Huntingtin Inclusion From A Stable Core, Sen Pei, Theresa C. Swayne, Jeffrey F. Morris, Lesley Emtage
Threshold Concentration And Random Collision Determine The Growth Of The Huntingtin Inclusion From A Stable Core, Sen Pei, Theresa C. Swayne, Jeffrey F. Morris, Lesley Emtage
Publications and Research
The processes underlying formation and growth of unfolded protein inclusions are relevant to neurodegenerative diseases but poorly characterized in living cells. In S. cerevisiae, inclusions formed by mutant huntingtin (mHtt) have some characteristics of biomolecular condensates but the physical nature and growth mechanisms of inclusion bodies remain unclear. We have probed the relationship between concentration and inclusion growth in vivo and find that growth of mHtt inclusions in living cells is triggered at a cytoplasmic threshold concentration, while reduction in cytoplasmic mHtt causes inclusions to shrink. The growth rate is consistent with incorporation of new material through collision and coalescence. …
A Cross-Level Information Transmission Network Forhierarchical Omics Data Integration And Phenotypeprediction From A New Genotype, Di He, Lei Xie
A Cross-Level Information Transmission Network Forhierarchical Omics Data Integration And Phenotypeprediction From A New Genotype, Di He, Lei Xie
Publications and Research
Motivation: An unsolved fundamental problem in biology is to predict phenotypes from a new genotype under environmental perturbations. The emergence of multiple omics data provides new opportunities but imposes great challenges in the predictive modeling of genotype-phenotype associations. Firstly, the high-dimensionality of genomics data and the lack of coherent labeled data often make the existing supervised learning techniques less successful. Secondly, it is challenging to integrate heterogeneous omics data from different resources. Finally,few works have explicitly modeled the information transmission from DNA to phenotype, which involves multiple intermediate molecular types. Higher-level features (e.g. gene expression) usually have stronger discriminative …
Decoding The Roles Of Astrocytes And Hedgehog Signaling In Medulloblastoma, Terence Teixeira Duarte, Silvia Aparecida Teixeira, Luis Gonzalez-Reyes, Rui Manuel Reis
Decoding The Roles Of Astrocytes And Hedgehog Signaling In Medulloblastoma, Terence Teixeira Duarte, Silvia Aparecida Teixeira, Luis Gonzalez-Reyes, Rui Manuel Reis
Publications and Research
The molecular evolution of medulloblastoma is more complex than previously imagined, as emerging evidence suggests that multiple interactions between the tumor cells and components of the tumor microenvironment (TME) are important for tumor promotion and progression. The identification of several molecular networks within the TME, which interact with tumoral cells, has provided new clues to understand the tumorigenic roles of many TME components as well as potential therapeutic targets. In this review, we discuss the most recent studies regarding the roles of astrocytes in supporting sonic hedgehog (SHH) subgroup medulloblastoma (MB) and provide an overview of MB progression through SHH …
A New Function For Amyloid-Like Interactions: Cross-Beta Aggregates Of Adhesins Form Cell-To-Cell Bonds, Peter N. Lipke, Marion Mathelié-Guinlet, Albertus Viljoen, Yves F. Dufrêne
A New Function For Amyloid-Like Interactions: Cross-Beta Aggregates Of Adhesins Form Cell-To-Cell Bonds, Peter N. Lipke, Marion Mathelié-Guinlet, Albertus Viljoen, Yves F. Dufrêne
Publications and Research
Amyloid structures assemble through a repeating type of bonding called “cross-β”, in which identical sequences in many protein molecules form β-sheets that interdigitate through side chain interactions. We review the structural characteristics of such bonds. Single cell force microscopy (SCFM) shows that yeast expressing Als5 adhesin from Candida albicans demonstrate the empirical characteristics of cross-β interactions. These properties include affinity for amyloid-binding dyes, birefringence, critical concentration dependence, repeating structure, and inhibition by anti-amyloid agents. We present a model for how cross-β bonds form in trans between two adhering cells. These characteristics also apply to other fungal adhesins, so the mechanism …
Agency Rescues Competition For Credit Assignment Among Predictive Cues From Adverse Learning Conditions, Mihwa Kang, Ingrid Reverte, Stephen Volz, Keith Kaufman, Salvatore Fevola, Anna Matarazzo, Fahd H. Alhazmi, Inmaculada Marquez, Mihaela D. Iordanova, Guillem R. Esber
Agency Rescues Competition For Credit Assignment Among Predictive Cues From Adverse Learning Conditions, Mihwa Kang, Ingrid Reverte, Stephen Volz, Keith Kaufman, Salvatore Fevola, Anna Matarazzo, Fahd H. Alhazmi, Inmaculada Marquez, Mihaela D. Iordanova, Guillem R. Esber
Publications and Research
A fundamental assumption of learning theories is that the credit assigned to predictive cues is not simply determined by their probability of reinforcement, but by their ability to compete with other cues present during learning. This assumption has guided behavioral and neural science research for decades, and tremendous empirical and theoretical advances have been made identifying the mechanisms of cue competition. However, when learning conditions are not optimal (e.g., when training is massed), cue competition is attenuated. This failure of the learning system exposes the individual’s vulnerability to form spurious associations in the real world. Here, we uncover that cue …
Case 3847 – Simopithecus Oswaldi Andrews, 1916 (Currently Theropithecus Oswaldi; Mammalia, Primates, Cercopithecidae), Proposed Conservation By Reversal Of Precedence With Cynocephalus Atlanticus Thomas, 1884., Eric Delson, David M. Alba, Stephen R. Frost, Dagmawit Abebe Getahun, Christopher C. Gilbert
Case 3847 – Simopithecus Oswaldi Andrews, 1916 (Currently Theropithecus Oswaldi; Mammalia, Primates, Cercopithecidae), Proposed Conservation By Reversal Of Precedence With Cynocephalus Atlanticus Thomas, 1884., Eric Delson, David M. Alba, Stephen R. Frost, Dagmawit Abebe Getahun, Christopher C. Gilbert
Publications and Research
The purpose of this application, under Articles 23.9.3 and 81.1 of the Code, is to conserve the usage of the species-group name Simopithecus oswaldi Andrews, 1916 by giving it precedence over its senior subjective synonym Cynocephalus atlanticus Thomas, 1884. Theropithecus is a common to dominant member of the extinct primate community across Africa after 4 million years ago (Jablonski & Frost, 2010) and often co-occurred with extinct humans (Hominini); fossils are also known rarely across Eurasia (Roberts et al., 2014). Most fossil samples are currently included in Theropithecus oswaldi (Andrews, 1916), which is often divided into chrono-geographic subspecies. Cynocephalus atlanticus …
Development Of An Online General Biology Open Educational Resource (Oer) Laboratory Manual, Dmitry Y. Brogun, Azure N. Faucette, Kristin Polizzotto, Farshad Tamari
Development Of An Online General Biology Open Educational Resource (Oer) Laboratory Manual, Dmitry Y. Brogun, Azure N. Faucette, Kristin Polizzotto, Farshad Tamari
Publications and Research
Currently, many academic institutions are using one or more variations of online modalities due to the COVID-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g., organismal biology). Additionally, resources for an online lab must be identified and curated from multiple sources, requiring intense demands on the instructors’ time. To meet this need and to overcome the financial burden of …
Griffithsin And Carrageenan Combination Results In Antiviral Synergy Against Sars-Cov-1 And 2 In A Pseudoviral Model, Sahar Alsaidi, Nadjet Cornejal, Oneil Mahoney, Claudia Melo, Neeharika Verma, Thierry Bonnaire, Theresa Chang, Barry R. O'Keefe, James Sailer, Thomas M. Zydowsky, Natalia Teleshova, José A. Fernández Romero
Griffithsin And Carrageenan Combination Results In Antiviral Synergy Against Sars-Cov-1 And 2 In A Pseudoviral Model, Sahar Alsaidi, Nadjet Cornejal, Oneil Mahoney, Claudia Melo, Neeharika Verma, Thierry Bonnaire, Theresa Chang, Barry R. O'Keefe, James Sailer, Thomas M. Zydowsky, Natalia Teleshova, José A. Fernández Romero
Publications and Research
Over 182 million confirmed cases of COVID-19 and more than 4 million deaths have been reported to date around the world. It is essential to identify broad-spectrum antiviral agents that may prevent or treat infections by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but also by other coronaviruses that may jump the species barrier in the future. We evaluated the antiviral selectivity of griffithsin and sulfated and non-sulfated polysaccharides against SARS-CoV-1 and SARS-CoV-2 using a cytotoxicity assay and a cell-based pseudoviral model. The half-maximal cytotoxic concentration (CC50) and half-maximal effective concentration (EC50) were determined for each compound, using a dose-response-inhibition …
Bcr Affinity Influences T-B Interactions And B Cell Development In Secondary Lymphoid Organs, Alec J. Wishnie, Tzippora Chwat-Edelstein, Mary Attaway, Bao Q. Vuong
Bcr Affinity Influences T-B Interactions And B Cell Development In Secondary Lymphoid Organs, Alec J. Wishnie, Tzippora Chwat-Edelstein, Mary Attaway, Bao Q. Vuong
Publications and Research
B cells produce high-affinity immunoglobulins (Igs), or antibodies, to eliminate foreign pathogens. Mature, naïve B cells expressing an antigen-specific cell surface Ig, or B cell receptor (BCR), are directed toward either an extrafollicular (EF) or germinal center (GC) response upon antigen binding. B cell interactions with CD4+ pre-T follicular helper (pre- Tfh) cells at the T-B border and effector Tfh cells in the B cell follicle and GC control B cell development in response to antigen. Here, we review recent studies demonstrating the role of B cell receptor (BCR) affinity in modulating T-B interactions and the subsequent differentiation of B …
Facial Diplegia: A Rare, Atypical Variant Of Guillain-Barré Syndrome And Ad26.Cov2.S Vaccine, Esha Jain, Krunal Pandav, Pratima Regmi, George Michel, Ida Altshuler
Facial Diplegia: A Rare, Atypical Variant Of Guillain-Barré Syndrome And Ad26.Cov2.S Vaccine, Esha Jain, Krunal Pandav, Pratima Regmi, George Michel, Ida Altshuler
Publications and Research
This potentially life-threatening disease poses an interesting perspective on adverse events that can occur or can be exacerbated following the Ad26.COV2.S (Johnson & Johnson) vaccine. The authors report findings in a 65-year-old female patient who experienced facial diplegia, an atypical variant of Guillain-Barré syndrome, two weeks after receiving the Ad26.COV2.S vaccine against coronavirus disease 2019. Post-approval pharmacovigilance of each vaccine helps better understand the long-term outcomes, and reporting adverse events is crucial for advancements in medical knowledge.
A Systematic Review And Meta-Analysis On The Efficacy Of Stem Cell Therapy On Bone Brittleness In Mouse Models Of Osteogenesis Imperfecta, Lauren Battle, Shoshana Yakar, Alessandra Carriero
A Systematic Review And Meta-Analysis On The Efficacy Of Stem Cell Therapy On Bone Brittleness In Mouse Models Of Osteogenesis Imperfecta, Lauren Battle, Shoshana Yakar, Alessandra Carriero
Publications and Research
There is no cure for osteogenesis imperfecta (OI), and current treatments can only partially correct the bone phenotype. Stem cell therapy holds potential to improve bone quality and quantity in OI. Here, we conduct a systematic review and meta-analysis of published studies to investigate the efficacy of stem cell therapy to rescue bone brittleness in mouse models of OI. Identified studies included bone marrow, mesenchymal stem cells, and human fetal stem cells. Effect size of fracture incidence, maximum load, stiffness, cortical thickness, bone volume fraction, and raw engraftment rates were pooled in a random-effects meta-analysis. Cell type, cell number, injection …
A Vision For Science Gateways: Bridging The Gap And Broadening The Outreach, Sandra Gesing, Steven R. Brandt, Shannon Bradley, Mark Potkewitz, Kirk F. Kee, Noreen Y. Whysel, Mark J. Perri, Sean B. Cleveland, Annalie Rugg, Jack A. Smith
A Vision For Science Gateways: Bridging The Gap And Broadening The Outreach, Sandra Gesing, Steven R. Brandt, Shannon Bradley, Mark Potkewitz, Kirk F. Kee, Noreen Y. Whysel, Mark J. Perri, Sean B. Cleveland, Annalie Rugg, Jack A. Smith
Publications and Research
The future for science gateways warrants exploration as we consider the possibilities that extend well beyond science and high performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways need to overcome in areas such as accessibility, usability and interoperability, and in the need for broader outreach by drawing insights from technology adoption research. We explore two particularly promising opportunities for gateways - computational social sciences and virtual reality – and make the case for the gateway community to be …
Notch Signaling Represses Cone Photoreceptor Formation Through The Regulation Of Retinal Progenitor Cell States, Xueqing Chen, Mark M. Emerson
Notch Signaling Represses Cone Photoreceptor Formation Through The Regulation Of Retinal Progenitor Cell States, Xueqing Chen, Mark M. Emerson
Publications and Research
Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized …
Nih Portfolio Of Unintentional Injury Research Among Racial And Ethnic Minority Children: Current Landscape And Future Opportunities, Maria Isabel Roldos, Tilda Farhat, Thomas Moehlman
Nih Portfolio Of Unintentional Injury Research Among Racial And Ethnic Minority Children: Current Landscape And Future Opportunities, Maria Isabel Roldos, Tilda Farhat, Thomas Moehlman
Publications and Research
Unintentional injuries (UIs) caused by accidental suffocation, burns, drowning, falls, poisoning, and motor vehicle accidents are the leading causes of morbidity and mortality among children (Dellinger and Gilchrist. Am J Lifestyle Med; 2017). Notable racial and ethnic disparities exist in accidental suffocation among infants and in motor vehicle injuries (MVI) among youth. The purpose of this study is to examine the National Institutes of Health's funded research projects addressing UIs, using a socioecological framework, and to determine whether funded projects align with key priorities for unintentional injuries among racial and ethnic minorities as identified by the research community. Between 2011 …
Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi
Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi
Publications and Research
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not. As pseudoknots can not be contained into two different blocks, this characterization allow us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Moreover we have extended the partitioning algorithm by classifying a pseudoknot as either recursive or non-recursive in order to continue with our research …
The Effects Of Climate And Demographic History In Shaping Genomic Variation Across Populations Of The Desert Horned Lizard (Phrynosoma Platyrhinos), Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe, Tereza Jezkova
The Effects Of Climate And Demographic History In Shaping Genomic Variation Across Populations Of The Desert Horned Lizard (Phrynosoma Platyrhinos), Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe, Tereza Jezkova
Publications and Research
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization …
Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly
Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly
Publications and Research
One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 …
Holding Space For Uncertainty And Vulnerability: Reclaiming Humanity In Teacher Education Through Contemplative | Equity Pedagogy, Malgorzata Powietrzynska, Linda Noble, Sharda O’Loughlin‑Boncamper, Aundrey Azeez
Holding Space For Uncertainty And Vulnerability: Reclaiming Humanity In Teacher Education Through Contemplative | Equity Pedagogy, Malgorzata Powietrzynska, Linda Noble, Sharda O’Loughlin‑Boncamper, Aundrey Azeez
Publications and Research
In this manuscript we describe our journey as two White coteachers conducting interpretive research with Black and Brown students in a remote-learning teacher preparation course in New York City. In the context of uncertainty, during the twin epidemics of COVID-19 and racial injustice, we explore how we reframed our contemplative pedagogy by embracing an equity-oriented framework. We share stories about moments of awakening drawn from spaces between us and our exceptional cohort of special education teachers – reflections about sensations, emotions, biases, and lived experiences as we embrace the identity of interbeing. Specifically, we explore transformations in our approach to …
Predicting Synchronized Gene Coexpression Patterns From Fibration Symmetries In Gene Regulatory Networks In Bacteria, Ian Leifer, Mishael Sánchez‑Pérez, Cecilia Ishida, Hernán A. Makse
Predicting Synchronized Gene Coexpression Patterns From Fibration Symmetries In Gene Regulatory Networks In Bacteria, Ian Leifer, Mishael Sánchez‑Pérez, Cecilia Ishida, Hernán A. Makse
Publications and Research
Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the question whether it is possible to predict gene synchronization from network structure alone. We have recently shown that synchronized gene expression can be predicted from symmetries in the gene regulatory networks described by the concept of symmetry fibrations. We showed that symmetry fibrations partition the genes into groups called fibers based on the symmetries of their ’input trees’, the set of paths in the network through which …
Learning Of Food Preferences: Mechanisms And Implications For Obesity & Metabolic Diseases, Hans-Rudolf Berthoud, Christopher D. Morrison, Karen Ackroff, Anthony Sclafani
Learning Of Food Preferences: Mechanisms And Implications For Obesity & Metabolic Diseases, Hans-Rudolf Berthoud, Christopher D. Morrison, Karen Ackroff, Anthony Sclafani
Publications and Research
Omnivores, including rodents and humans, compose their diets from a wide variety of potential foods. Beyond the guidance of a few basic orosensory biases such as attraction to sweet and avoidance of bitter, they have limited innate dietary knowledge and must learn to prefer foods based on their flavors and postoral effects. This review focuses on postoral nutrient sensing and signaling as an essential part of the reward system that shapes preferences for the associated flavors of foods. We discuss the extensive array of sensors in the gastrointestinal system and the vagal pathways conveying information about ingested nutrients to the …
Fingerprinting The Cretaceous-Paleogene Boundary Impact With Zn Isotopes, Ryan Mathur, Brandon Mahan, Marissa Spencer, Linda Godfrey, Neil Landman, Matthew Garb, D. Graham Pearson, Sheng-Ao Liu, Francisca E. Oboh-Ikuenobe
Fingerprinting The Cretaceous-Paleogene Boundary Impact With Zn Isotopes, Ryan Mathur, Brandon Mahan, Marissa Spencer, Linda Godfrey, Neil Landman, Matthew Garb, D. Graham Pearson, Sheng-Ao Liu, Francisca E. Oboh-Ikuenobe
Publications and Research
Numerous geochemical anomalies exist at the K-Pg boundary that indicate the addition of extraterrestrial materials; however, none fingerprint volatilization, a key process that occurs during large bolide impacts. Stable Zn isotopes are an exceptional indicator of volatilityrelated processes, where partial vaporization of Zn leaves the residuum enriched in its heavy isotopes. Here, we present Zn isotope data for sedimentary rock layers of the K-Pg boundary, which display heavier Zn isotope compositions and lower Zn concentrations relative to surrounding sedimentary rocks, the carbonate platform at the impact site, and most carbonaceous chondrites. Neither volcanic events nor secondary alteration during weathering and …