Physical Sciences and Mathematics Commons^™

A Review Of Theropithecus Oswaldi With The Proposal Of A New Subspecies, Dagmawit Abebe Getahun, Eric Delson, Chalachew Mesfin Seyoum

Publications and Research

Theropithecus oswaldi darti, as currently understood, is the oldest Theropithecus taxon in the fossil record and the earliest subspecies in the Theropithecus oswaldi lineage. Theropithecus oswaldi darti is typified at the site of Makapansgat in South Africa, and a similar form (T. o. cf. darti) is usually recognized at Hadar, Dikika, some Middle Awash localities, and Woranso-Mille in Ethiopia. This taxon is also tentatively believed to occur in Kenya at Kanam and Koobi Fora and in Member C of the Shungura Formation in Ethiopia. While there is a general consensus that the East African ‘darti’ specimens are …

Small Molecule Modulation Of Microbiota: A Systems Pharmacology Perspective, Qiao Liu, Bohyun Lee, Lei Xie

Publications and Research

Background

Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome signatures. However, emerging endeavors in small-molecule microbiome drug discovery continue to follow a conventional “one-drug-one-target-one-disease” process. A systematic pharmacology approach that would suppress multiple interacting pathogenic species in the microbiome, could offer an attractive alternative solution.

Results

We construct a disease-centric signed microbe–microbe interaction network using curated microbe metabolite information and their effects on host. We develop a Signed Random Walk with Restart algorithm for the accurate prediction of effect of microbes …

Student Self-Grading Form, Brett Whysel

Open Educational Resources

This is a word document that students use at the beginning, midpoint, and end of a semester to set relevant goals, measure progress towards goals, and self-grade. It is intended to build motivation, metacognition, and accountability. Instructors may use it on its own or to supplement other assessment tools, and improve the accuracy, validity, and fairness of final grades.

Positive Rate-Dependent Action Potential Prolongation By Modulating Potassium Ion Channels, Candido Cabo

Publications and Research

Pharmacological agents that prolong action potential duration (APD) to a larger extent at slow rates than at the fast excitation rates typical of ventricular tachycardia exhibit reverse rate dependence. Reverse rate dependence has been linked to the lack of efficacy of class III agents at preventing arrhythmias because the doses required to have an anti-arrhythmic effect at fast rates may have pro-arrhythmic effects at slow rates due to an excessive APD prolongation. In this report we show that, in computer models of the ventricular action potential, APD prolongation by accelerating phase 2 repolarization (by increasing I_Ks) and decelerating …

Emotion Recognition With Audio, Video, Eeg, And Emg: A Dataset And Baseline Approaches, Jin Chen, Tony Ro, Zhigang Zhu

Publications and Research

This paper describes a new posed multimodal emotional dataset and compares human emotion classification based on four different modalities - audio, video, electromyography (EMG), and electroencephalography (EEG). The results are reported with several baseline approaches using various feature extraction techniques and machine-learning algorithms. First, we collected a dataset from 11 human subjects expressing six basic emotions and one neutral emotion. We then extracted features from each modality using principal component analysis, autoencoder, convolution network, and mel-frequency cepstral coefficient (MFCC), some unique to individual modalities. A number of baseline models have been applied to compare the classification performance in emotion recognition, …

A Call For The Library Community To Deploy Best Practices Toward A Database For Biocultural Knowledge Relating To Climate Change, Martha B. Lerski

Publications and Research

Abstract

Purpose – In this paper, a call to the library and information science community to support documentation and conservation of cultural and biocultural heritage has been presented.

Design/methodology/approach – Based in existing Literature, this proposal is generative and descriptive— rather than prescriptive—regarding precisely how libraries should collaborate to employ technical and ethical best practices to provide access to vital data, research and cultural narratives relating to climate.

Findings – COVID-19 and climate destruction signal urgent global challenges. Library best practices are positioned to respond to climate change. Literature indicates how libraries preserve, share and cross-link cultural and scientific knowledge. …

Technical Note: Novel Estimates Of The Leaf Relative Uptake Rate Of Carbonyl Sulfide From Optimality Theory, Georg Wohlfahrt, Albin Hammerle, Felix M. Spielmann, Florian Kitz, Chuixiang Yi

Publications and Research

In order to estimate the gross primary productivity (GPP) of terrestrial ecosystems from the canopy uptake of carbonyl sulfide (COS), the leaf relative uptake rate (LRU) of COS with respect to carbon dioxide needs to be known a priori. Currently, the variability of the LRU between plant species in different biomes of the world is poorly understood, making the choice of an appropriate LRU uncertain and hampering further progress towards developing COS as an alternative tracer of GPP. Here we propose a novel approach for estimating LRU based on plant optimality principles, validate it against in situ leaf gas exchange …

Satellite Evidence Of Canopy-Height Dependence Of Forest Drought Resistance In Southwestern China, Peipei Xu, Wei Fang, Tao Zhou, Hu Li, Xiang Zhao, Spencer Berman, Ting Zhang, Chuixiang Yi

Publications and Research

The frequency and intensity of drought events are increasing with warming climate, which has resulted in worldwide forest mortality. Previous studies have reached a general consensus on the size-dependency of forest resistance to drought, but further understanding at a local scale remains ambiguous with conflicting evidence. In this study, we assessed the impact of canopy height on forest drought resistance in the broadleaf deciduous forest of southwestern China for the 2010 extreme drought event using linear regression and a random forest (RF) model. Drought condition was quantified with standardized precipitation evapotranspiration index (SPEI) and drought resistance was measured with the …

The Naming Of Homo Bodoensis By Roksandic And Colleagues Does Not Resolve Issues Surrounding Middle Pleistocene Human Evolution, Eric Delson, Chris Stringer

Publications and Research

Roksandic et al. (2022) proposed the new species name Homo bodoensis as a replacement name for Homo rhodesiensis Woodward, 1921, because they felt it was poorly and variably defined and was linked to sociopolitical baggage. However, the International Code of Zoological Nomenclature includes regulations on how and when such name changes are allowed, and Roksandic et al.'s arguments meet none of these requirements. It is not permitted to change a name solely because of variable (or erroneous) later use once it has been originally defined correctly, nor can a name be modified because it is offensive to one or more …

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Globe Mosquito Habitat Mapper Citizen Science Data 2017–2020, Russanne Low, Rebecca Boger, Peder Nelson, Matteo Kimura

Publications and Research

The GLOBE Program's GLOBE Observer application is a free citizen science mobile data collection and visualization tool compatible with iOS and Android operating systems. Citizen scientists armed with the app can report the mosquito larval habitats they identify using the GLOBE Mosquito Habitat Mapper tool. This data can complement the climate, weather, and land cover data obtained from satellite measurements by scientists who develop risk models for mosquito-borne diseases. Public participation in mosquito surveillance research provides the opportunity to obtain the volume, velocity and variety of data needed to fight the threat of vector-borne diseases, especially in under-resourced communities with …

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 …

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 …

Pattern Of Use Of Electronic Health Record (Ehr) Among The Chronically Ill: A Health Information National Trend Survey (Hints) Analysis, Rose Calixte, Sumaiya Islam, Zainab Toteh Osakwe, Argelis Rivera, Marlene Camacho-Rivera

Publications and Research

Effective patient–provider communication is a cornerstone of patient-centered care. Patient portals provide an effective method for secure communication between patients or their proxies and their health care providers. With greater acceptability of patient portals in private practices, patients have a unique opportunity to manage their health care needs. However, studies have shown that less than 50% of patients reported accessing the electronic health record (EHR) in a 12-month period. We used HINTS 5 cycle 1 and cycle 2 to assess disparities among US residents 18 and older with any chronic condition regarding the use of EHR for secure direct messaging …

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

My Interdisciplinary Perspective On Climate Change [Natural Sciences], Richa Gupta, Tuli Chatterji, Tao Chen, Rebecca Schwartz

Open Educational Resources

This assignment titled “My Interdisciplinary Perspective on Climate Change” was developed in Fall 2020 as the signature assignment of the STEM Learning Community LC50 for students enrolled in the Biology program of the Natural Sciences department, at LaGuardia Community College, CUNY. The assignment targets Integrative Learning and Global Learning Core Competencies, and Digital/Oral Communication Abilities.

For this STEM Cluster, “Climate Change” is the shared theme that connects learning from the different disciplines and helps build students’ overall knowledge on an imperative issue that our planet currently faces. Work on this assignment entails a narrated digital student presentation on the various …

Dom Degradation By Light And Microbes Along The Yukon River‑Coastal Ocean Continuum, Brice K. Grunert, Maria Tzortziou, Patrick Neale, Alana Menendez, Peter Hernes

Publications and Research

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure …

Intangible Cultural Heritage: A Benefit To Climate-Displaced And Host Communities, Gül Aktürk, Martha B. Lerski

Publications and Research

Climate change is borderless, and its impacts are not shared equally by all communities. It causes an imbalance between people by creating a more desirable living environment for some societies while erasing settlements and shelters of some others. Due to floods, sea level rise, destructive storms, drought, and slow-onset factors such as salinization of water and soil, people lose their lands, homes, and natural resources. Catastrophic events force people to move voluntarily or involuntarily. The relocation of communities is a debatable climate adaptation measure which requires utmost care with human rights, ethics, and psychological well-being of individuals upon the issues …

The Effects Of Late Spring Frost On Forest And Landscape Health And Recovery Of The Black Rock Forest, New York, Caroline Eco, Oliver Imhans, Aaron Davitt, Andrew B. Reinmann

Publications and Research

Projected changes in climate are expected to increase the frequency of late spring frost events in the Northeast US. Such events can be harmful to trees because freezing temperatures that occur after leaf-out can damage or kill young leaves. The resultant defoliation typically forces a second flush of leaves, but delays canopy development, which in turn delays the onset of canopy carbon uptake and alters canopy thermal properties. In this study, we analyzed a recent freeze event that occurred on 8-9 May 2020 (DOY 129-130) at Black Rock Forest (BRF), which is in the Hudson Highlands of southeastern New York …

Species In Vernal Pools: Anova, Lisa Manne

Open Educational Resources

A one-way analysis of variance exercise using data on species diversities from vernal pools.Data are from vernal pools in Willowbrook Park (adjacent to College of Staten Island's campus) in spring.

The typical ANOVA gives a straightforward result (significant anova, easily-interpreted Tukey-Kramer analysis). This data set requires more nuanced interpretation, as the ANOVA is marginally significant, and Tukey-Kramer yields one significant pairwise comparison between groups. Relative lack of variation within groups explains this apparent enigma.

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

Accessibility: Disabilities Treasure Hunt, Devorah Kletenik

Open Educational Resources

This is a treasure hunt game that simulates various disabilities and gives a sense of how frustrating non-accessible content can be for people with disabilities. Suitable for a general audience, no programming experience necessary.

An editable copy is also given, along with ideas about how to make it more accessible.

Potential Solar Replacement Of Hydroelectricity To Reopen Rivers: Maine As A Case Example, Shailesh Sharma, John Waldman

Publications and Research

Hydroelectricity provides 6% of U.S. electrical power needs, but hydro-dams also cause environmental harm, including the retardation or complete blockage of spawning runs of anadromous fishes. To facilitate fish movements, engineered-fishways have long been used but many have performed poorly. Dam-removal is the most effective way of restoring dwindling migratory fish populations by allowing unrestricted pathways to their spawning areas and for the downstream migrations of post-spawning adults and juveniles. However, removals of hydro-dams result in a loss of electricity production. For the replacement of energy foregone from hydro-dam removals, various alternative energy installations are now feasible. We present one-to-one …

African Land Mammal Ages, John Van Couvering, Eric Delson

Publications and Research

We define 17 African land mammal ages, or AFLMAs, covering the Cenozoic record of the Afro-arabian continent, the planet’s second largest land mass. While fossiliferous deposits are absent on the eroded plateau of the continent’s interior, almost 800 fossil genera from over 350 locations have now been identified in coastal deposits, karst caves, and in the Neogene rift valleys. Given a well-developed geochronologic framework, together with continuing revision to the fossil record—both stimulated by the story of human evolution in Africa—and also to compensate for the variation in fossil ecosystems across such great distances, the AFLMAs are biochronological units defined …

Extending Import Detection Algorithms For Concept Import From Two To Three Biomedical Terminologies, Vipina K. Keloth, James Geller, Yan Chen, Julia Xu

Publications and Research

Background: While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology.

Methods: In this paper, we are extending …

Understanding Of Aerosol Transmission Of Covid 19 In Indoor Environments, Adama Barro, Cathal O'Toole, Jacob S. Lopez, Matthew Quinones, Sherene Moore

Publications and Research

Our reason for discussing severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) or 2019 novel corona virus (Covid-19), is to understand its aerosol transmission characteristics in indoor spaces and to mitigate further spread of this disease by designing a new HVAC system. The problem that we are tackling is the spread of covid-19 droplets through aerosol transmission by looking at potential engineering solutions to the existing HVAC systems. The purpose is to eradicate the spread of the COVID-19 by testing indoor spaces in an effort to understand the effectiveness of ventilation controls. We believe that scientists and engineers have not …

Data Analysis And Visualizations Of Drosophila Behavioral Phases, Xiaona Zhou

Publications and Research

We analyze drosophila behavioral data from the neuroscience labs of Professor Maria de la Paz Fernandez, Barnard College of Columbia University, and Professor Orie Shafer, the Neuroscience Initiative of the CUNY Advanced Science Research Center. The main goal of this project is to create algorithms for analyzing and visualizing the average activity of drosophila across a specified number of days and across all live flies and use this analysis to calibrate a smoothing filter to be applied to the raw fly activity so that the drosophila behavioral phases can be computed and visualized. We also investigate how to compute and …

Evolutionary Algorithms Converge Towards Evolved Biological Photonic Structures, Mamadou Aliou Barry, Vincent Berthier, Bobo D. Wilts, Marie-Claire Cambourieux, Pauline Bennet, Rémi Pollès, Olivier Teytaud, Emmanuel Centeno, Nicolas Biais, Antoine Moreau

Publications and Research

Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution in order to more efciently refect, absorb or scatter light. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these complex naturally occurring structures. Using evolutionary algorithms inspired by natural evolution and performing particular optimizations (maximize refection for a given wavelength, for a broad range of wavelength or maximize the scattering of light), we have retrieved the most stereotypical natural photonic structures. Whether those structures are Bragg mirrors, chirped dielectric mirrors or the gratings on top of …

Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse

Publications and Research

We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks …