Life Sciences Commons^™

The International Conference On Intelligent Biology And Medicine (Icibm) 2018: Bioinformatics Towards Translational Applications, Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhuan Ruan, Degui Zhi

Publications and Research

The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks, which covered a wild range of aspects of bioinformatics, medical informatics, systems biology and intelligent computing. Here, we summarize nine research articles selected for publishing in BMC Bioinformatics.

Instances Of Influenza In The United States Visualized, Parth Patel

Publications and Research

The Tycho Project collects large data sets related to healthcare and in particular, instances and geographical information of diseases. We look at the instance counts and locations of Influenza from 1919-1951 across the United States. We hope to find seasonal and geographical insight to the spread of the disease.

Microbial Diversity In Urban Environments: Concern For Antibiotic Resistance, Ality Aghedo, Mangala Tawde, Nazrul I. Khandaker

Publications and Research

We are almost oblivious to the presence of microorganisms in our daily lives, but they exist and come into contact with us all the time. While some bacteria are harmless, and even beneficial, other bacteria can cause infections. A common treatment to bacterial infections is antibiotics and the success of an antibiotic depends on the resistance of the bacteria to the antibiotic. We conducted experiments to identify the types of bacteria that can be found on surfaces or within soil environments that come into contact with a vast number of people on a daily basis and how this can affect …

Season-Ahead Forecasting Of Water Storage And Irrigation Requirements – An Application To The Southwest Monsoon In India, Arun Ravindranath, Naresh Devineni, Upmanu Lall, Paulina Concha Larrauri

Publications and Research

Water risk management is a ubiquitous challenge faced by stakeholders in the water or agricultural sector. We present a methodological framework for forecasting water storage requirements and present an application of this methodology to risk assessment in India. The application focused on forecasting crop water stress for potatoes grown during the monsoon season in the Satara district of Maharashtra. Pre-season large-scale climate predictors used to forecast water stress were selected based on an exhaustive search method that evaluates for highest ranked probability skill score and lowest root-mean-squared error in a leave-one-out cross-validation mode. Adaptive forecasts were made in the years …

A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm For Delicate Deep-Sea Biological Exploration, Brennan T. Phillips, Kaitlyn P. Becker, Shunichi Kurumaya, Kevin C. Galloway, Griffin Whittredge, Daniel M. Vogt, Clark B. Teeple, Michelle H. Rosen, Vincent A. Pieribone, David F. Gruber, Robert J. Wood

Publications and Research

Modern marine biologists seeking to study or interact with deep-sea organisms are confronted with few options beyond industrial robotic arms, claws, and suction samplers. This limits biological interactions to a subset of “rugged” and mostly immotile fauna. As the deep sea is one of the most biologically diverse and least studied ecosystems on the planet, there is much room for innovation in facilitating delicate interactions with a multitude of organisms. The biodiversity and physiology of shallow marine systems, such as coral reefs, are common study targets due to the easier nature of access; SCUBA diving allows for in situ delicate …

The Role Of Proton Transport In Gating Current In A Voltage Gated Ion Channel, As Shown By Quantum Calculations, Alisher M. Kariev, Michael E. Green

Publications and Research

Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGIC) to carry Na⁺ and K⁺ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently the structure of a number of VGIC was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains …

Digital Storytelling [Natural Sciences], Preethi Radhakrishnan

Open Educational Resources

A well-crafted and executed storytelling assignment can serve as an efficient and engaging learning activity which targets the three highest levels of Blooms’ taxonomy which are to Create, Evaluate and Analyze. This digital storytelling assignment is part of a signature assignment series (Stage 1) conducted in all courses of the First Year Seminar for Natural Sciences (NSF101). Students begin collecting pictures and videos for their assignment from the 3^rd week of the semester on a flash drive. During the fourth week of the semester, the instructor first describes the storytelling process and stages. This is followed by learning around …

Investigation Of Biogeochemical Mechanisms Of Greenhouse Gas Production In The Urban Hudson River Estuary, Brian Alan Brigham

Dissertations, Theses, and Capstone Projects

Coastal megacities deposit significant amounts of carbon (C), nitrogen (N) and other pollutants into surrounding waters. These inputs, including wastewater and surface water runoff, may affect estuarine and adjacent wetland biogeochemical cycles, microbial production and ultimately greenhouse gas (GHG) efflux. In many megacities pollutant loading is typically greatest after periods of precipitation when the volume of wastewater and storm water runoff exceeds local sanitation capacity, resulting in the discharge of raw sewage into adjacent waters. These combined sewage overflow (CSO) events have received considerable attention primarily due to their potential impact on human health and eutrophication. However, whether these events …

Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz

Dissertations, Theses, and Capstone Projects

In this thesis I show that greatly increasing the magnitude of a protein’s net charge using surface supercharging transforms that protein into a ligand-gated or counterion-gated conformational molecular switch. To demonstrate this I first modified the designed helical bundle hemoprotein H4 using simple molecular modeling, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. Due to the high surface charge density, ligand binding to this protein is allosterically activated by low concentrations of divalent cations and the polyamine spermine. …

Ulva Spp. Bloom Dynamics In A Hyper-Eutrophic Estuary: Jamaica Bay, New York, Annesia Lamb

Dissertations, Theses, and Capstone Projects

In this dissertation, I present three studies that further our understanding of macroalgae identity, growth, and proliferation. Eutrophication is prevalent in shallow coastal ecosystems world-wide. One of the ecosystem consequences is the development of a bloom forming green marine macroalgae, Ulva spp. Ulva can have negative effects such as Zostera spp. degradation, fish, and shellfish declines. I performed assessments of (1) identity of the bloom-forming Ulva and other macroalgae assemblage, (2) physical, chemical, and biological drivers of Ulva bloom growth and proliferation, and (3) optimal irradiance and temperature requirements for early growth stages in Ulva linza.

The first study …

Nanostructured Fibers As A Versatile Photonic Platform: Radiative Cooling And Waveguiding Through Transverse Anderson Localization, Norman Nan Shi, Cheng-Chia Tsai, Michael J. Carter, Jyotirmoy Mandal, Adam C. Overvig, Matthew Y. Sfeir, Ming Lu, Catherine L. Craig, Gary D. Bernard, Yuan Yang, Nanfang Yu

Publications and Research

Broadband high reflectance in nature is often the result of randomly, three-dimensionally structured materials. This study explores unique optical properties associated with one-dimensional nanostructures discovered in silk cocoon fibers of the comet moth, Argema mittrei. The fibers are populated with a high density of air voids randomly distributed across the fiber cross-section but are invariant along the fiber. These filamentary air voids strongly scatter light in the solar spectrum. A single silk fiber measuring ~50 μm thick can reflect 66% of incoming solar radiation, and this, together with the fibers' high emissivity of 0.88 in the mid-infrared range, allows …

Career/Interview Project, Kevin Mark

Open Educational Resources

Two of the core competencies designated for The First Year Seminar Liberal Arts Math and Science (LMF 101) course are Integrative Learning and Global Learning along with oral communication. These abilities are exercised by students in the Career/Interview Presentation project. The main goal of the assignment is to promote student networking within the scientific community through interviews with an expert in the field. Also the FYS students will conduct background research about their career choices and use their findings to determine if they can be realized when interviewing a professional. The assignment is scaffolded whereby students will learn to use …

Introduction To Data Analysis Using Excel And Lab Report Writing Using Lagcc Institution Data, Kevin Mark

Open Educational Resources

Objectives

Part 1: An Introduction to Data Analysis Using Excel

1. To interpret, summarize and present numerical data using the digital tool Microsoft program Excel.
2. To plot numerical data as a graph and determine an equation of a line. In addition, using the appropriate formatting functions to label your graph and creating a best fit line.

Part 2: Lab Report Writing Using LaGCC Institutional Data

1. To communicate your interpretations of research data. This is done writing discussions and conclusions (using scientific language) and is often accompanied by data tables and graphs.
2. To use your Microsoft Excel graphing skills to interpret, inquire …

Women In Science: Why So Few? [Liberal Arts: Math And Science], Reem Jaafar, Benjamin J. Taylor

Open Educational Resources

This assigment was developed in the context of LaGuardia’s Center for Teaching and Learning sponsored Learning Matters mini grant “Connection Between First Year Seminar and Capstone Learning Experiences.” It provides Liberal Arts experience to students across the academic spectrum and is designed for students in LMF 101 (First-Year Seminar for Liberal Arts: Math & Science) and is conducted in conjunction with students from a capstone course, LIB 200 (Science, Technology, and Humanism). The assignment aligns with the Inquiry and Problem-Solving Core Competency and the Written Ability. In this assignment, LMF 101 students research and read several articles centered on the …

Hip Extensor Mechanics And The Evolution Of Walking And Climbing Capabilities In Humans, Apes, And Fossil Hominins, Elaine E. Kozma, Nicole M. Webb, William Harcourt-Smith, David A. Raichlen, Kristiaan D’Août, Mary H. Brown, Emma M. Finestone, Stephen R. Ross, Peter Aerts, Herman Pontzer

Publications and Research

The evolutionary emergence of humans’ remarkably economical walking gait remains a focus of research and debate, but experi- mentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental mea- surements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal–terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by …

The Therapeutic Potential Of Natural Products From Vaccinium Berries For Viral And Lung Diseases Through An Improved Lc-Ms-Based Chemometric Approach, Vanya I. Petrova

Dissertations, Theses, and Capstone Projects

Smoking is a global epidemic that creates serious health and economic burden. It is the primary, preventative factor for the majority of causes of death worldwide. Analysis of publicly available data revealed that smoking prevalence rates among the youth in developing countries, especially in Bulgaria, are alarmingly high. The Bulgarian population has one of the highest percentages of smokers and the second highest rate among teenage girls. Consequently, chronic diseases affected by smoking, such as chronic obstructive pulmonary disorder (COPD), have been increasing there in the last five years. Poland, on the other hand, is an exemplary outlier for the …

Cooperative Standing-Horizontalstanding Reentrant Transition For Numerous Solid Particles Under External Vibration, Satoshi Takatori, Hikari Baba, Takatoshi Ichino, Chwen-Yang Shew, Kenichi Yoshikawa

Publications and Research

We report the collective behavior of numerous plastic bolt-like particles exhibiting one of two distinct states, either standing stationary or horizontal accompanied by tumbling motion, when placed on a horizontal plate undergoing sinusoidal vertical vibration. Experimentally, we prepared an initial state in which all of the particles were standing except for a single particle that was placed at the center of the plate. Under continuous vertical vibration, the initially horizontal particle triggers neighboring particles to fall over into a horizontal state through tumbling-induced collision, and this effect gradually spreads to all of the particles, i.e., the number of horizontal particles …

Regulation Of Radioactive Fracking Waste, Elizabeth Ann Glass Geltman, Nichole Leclair

Publications and Research

Natural gas extracted form shale reached record production totals in 2015 in the United States and the US Energy Information Administration (EIA) forecasts natural gas production will continue to increase. Wastes from shale gas extraction can contain the radioactive isotopes radium-226 (Ra-226) and radium-228 (Ra-228), which decay further into radon (Rn). Exposure to radon, a form of naturally occurring radioactive materials (NORM), is the leading cause of lung cancer in the United States, after smoking. This article explores how states handle the disposal of technologically enhanced naturally occurring radioactive materials (TENORM) and/or NORM waste from oil and gas operations to …