Physical Sciences and Mathematics 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.

Nano-Based Systems And Biomacromolecules As Carriers For Metallodrugs In Anticancer Therapy, Mina Poursharifi, Marek T. Wlodarczyk, Aneta J. Mieszawska

Publications and Research

Since the discovery of cisplatin and its potency in anticancer therapy, the development of metallodrugs has been an active area of research. The large choice of transition metals, oxidation states, coordinating ligands, and different geometries, allows for the design of metal-based agents with unique mechanisms of action. Many metallodrugs, such as titanium, ruthenium, gallium, tin, gold, and copper-based complexes have been found to have anticancer activities. However, biological application of these agents necessitates aqueous solubility and low systemic toxicity. This minireview highlights the emerging strategies to facilitate the in vivo application of metallodrugs, aimed at enhancing their solubility and bioavailability, …

Open Source Foundations For Spatial Decision Support Systems, Jochen Albrecht

Publications and Research

Spatial Decision Support Systems (SDSS) were a hot topic in the 1990s, when researchers tried to imbue GIS with additional decision support features. Successful practical developments such as HAZUS or CommunityViz have since been built, based on commercial desktop software and without much heed for theory other than what underlies their process models. Others, like UrbanSim, have been completely overhauled twice but without much external scrutiny. Both the practical and the theoretical foundations of decision support systems have developed considerably over the past 20 years. This article presents an overview of these developments and then looks at what corresponding tools …

Computational Techniques For Scattering Amplitudes, Juliano A. Everett

Publications and Research

Scattering amplitudes in quantum field theory can be described as the probability of a scattering process to happen within a high energy particle interaction, as well as a bridge between experimental measurements and the prediction of the theory.

In this research project, we explore the Standard Model of Particle Theory, it’s representation in terms of Feynman diagrams and the algebraic formulas associated with each combination.

Using the FeynArts program as a tool for generating Feynman diagrams, we evaluate the expressions of a set of physical processes, and explain why these techniques become necessary to achieve this goal.

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.

Historical Effects Of Electronic Interfaces, G James Mitchell

Publications and Research

Electronic interfaces are a primary tool for most professional and personal communication currently happening. Electronics, like the human mind, are limited by the understanding of executing will, or commands. This can be characterized as “interface limitations” of digital technology. Identifying this bottleneck in technological development has been critical in historical changes to both hardware and software technology. Recent medical research examines a novel user interface to reduce task load. I hypothesize, interface developments that take cues from nonverbal human communication enhance and sustain the significance of those technologies in society. By examining pivotal moments of historical technology we can identify …

Chemistry Student Attitudes And Utilization Of Office Hours, Dieng Barbacar, Edgar Gomez, Andre Rodriguez

Publications and Research

While research has demonstrated that faculty-student interactions increase retention and graduation rates, faculty often report that their office hours are underutilized. To better understand students’ attitudes, usage and plans towards faculty hours a survey was administered in the second to third week of the fall 2018 semester to students in 5 sections of general chemistry courses. The goal was to better understand how students perceive the benefits and hindrances of office hours, along with current or planned attendance. Prior to survey administration, it was speculated that not attending office hours could be because they were not scheduled at a convenient …

Analysis Of Land Surface Temperature Over Urban Landcover Types Using Satellite Remote Sensing And Ground-Based Applications, Makini Valentine, Justine Ginchereau

Publications and Research

Urban areas have discrete differences in their land surface temperatures (LST) compared to rural areas. These regions are covered with impermeable materials with less vegetation and moisture. Consequently, this phenomenon causes major thermal intensities of different land surfaces, negatively impact people and environment. The objective of this project is to examine and to compare land surface temperature obtained from in-situ data and satellite-based observations in order to understand the diurnal variation and heat transfer at each surface type. The study utilizes series of hand held thermal infrared cameras and one Unmanned Aerial Vehicle (UAV) infrared camera to find land surface …

Receiver-Initiated Handshaking Mac Based On Traffic Estimation For Underwater Sensor Networks, Yuan Dong, Lina Pu, Yu Luo, Zheng Peng, Haining Mo, Yun Meng, Yi Zhao, Yuzhi Zhang

Publications and Research

In underwater sensor networks (UWSNs), the unique characteristics of acoustic channels have posed great challenges for the design of medium access control (MAC) protocols. The long propagation delay problem has been widely explored in recent literature. However,the long preamble problem with acoustic modems revealed in real experiments brings new challenges to underwater MAC design. The overhead of control messages in handshaking-based protocols becomes significant due to the long preamble in underwater acoustic modems. To address this problem, we advocate the receiver-initiated handshaking method with parallel reservation to improve the handshaking efficiency. Despite some existing works along this direction, the data …

Impact Of Fiber Parameters On Edfa And/Or Raman Amplified High-Spectral-Efficiency Coherent Wdm Transmissions, Lufeng Leng

Publications and Research

The impact of fiber properties is investigated for coherent systems employing polarization-division multiplexed high-level quadrature amplitude modulation, wavelength-division multiplexing, and erbium-doped fiber amplifier and/or distributed Raman amplification. This is done by comparing the performances of fiber links of various attenuation coefficients and effective areas via experimentally verified analytical methods. Results show that the excess noise, which originates at amplifiers compensating for the losses of filters and switches located between fiber spans, can weaken or even diminish the performance enhancement brought about by lowering the fiber attenuation coefficient, especially if distributed Raman amplification is employed. This leads to the difference in …

Synthesis And Evaluation Of Troponoids As A New Class Of Antibiotics, Feng Cao, Cari Orth, Maureen J. Donlin, Patrick Adegboyega, Marvin J. Meyers, Ryan P. Murelli, Mohamed Elagawany, Bahaa Elgendy, John E. Tavis

Publications and Research

Novel antibiotics are urgently needed. The troponoids [tropones, tropolones, and α-hydroxytropolones (α-HT)] can have anti-bacterial activity. We synthesized or purchased 92 troponoids and evaluated their antibacterial activities against Staphylococcus aureus, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. Preliminary hits were assessed for minimum inhibitory concentrations (MIC80) and cytotoxicity (CC50) against human hepatoma cells. Sixteen troponoids inhibited S. aureus/E. coli/ A. baumannii growth by ≥80% growth at <30 >μM with CC50 values >50 μM. Two selected tropolones (63 and 285) inhibited 18 methicillin-resistant S. aureus (MRSA) strains with similar MIC80 values as against a reference strain. Two selected thiotropolones (284 and 363) …

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 …

An Overview Of Smartwater Management System: Strategic Potential In Bangladesh, Muhammad Qumrul Hassan, Mir F. Karim, Nazrul I. Khandaker, Jowaher Raza

Publications and Research

Water loss management is becoming an increasingly important as supplies are stressed by population growth or water scarcity. A SmartWater system ensures optimum consumption and prediction of future water use. Bangladesh is one of the most vulnerable countries due to global climate change considering its rapid urbanization, inequitable land use, low income and greater reliance on climate sensitive sectors, particularly agriculture. Agricultural lands used for cropping and livestock rearing are more susceptible to degradation than non-agricultural lands. Most farmers irrigate through flooding, losing up to 75% of water to evaporation and creating a substantial drawdown of much needed water for …

The Status Of Engineering Geology: Constraints On Infrastructure Development In Bangladesh, Mir Fazlul Karim, Muhammad Qumrul Hassan, Nazrul I. Khandaker, Masud Ahmed, Belal Ahmed Sayeed

Publications and Research

In recent years, megacity Dhaka is known to have one of the fastest urban population growths in Bangladesh. The population in Dhaka and other megacities has increased from 7 to 50 million during the last four decades. The rapid rate of urban population growth, along with the extreme paucity of real-estate for new infrastructure development or upgrading existing facilities, is already exacerbating the situation for the city planners and exerting tremendous pressure to come-up with viable solutions. Although practice of engineering geology, geotechnical exploration, and testing exists in Bangladesh; the system has still yet to adopt controlled quality standards with …

Lithologic Constraints On The Hydrological Parameters Of Regional Aquifers In The Ibb Province, West-Central Region Of Yemen (Middle East), Malek Shami, Zarine Ali, Wedad Abdurabu, Nazrul I. Khandaker, Stanley Schleifer

Publications and Research

The lithology of the Ibb Province Yemen (Middle East) consists of Precambrian gneissic bedrocks with post-tectonic intrusions of granite and granodiorite. The overall topography is dominated by extensive volcanic extrusions that randomly surround Ibb Province with minimal Mesozoic sedimentary outcrops. According to the Yemen Geological Survey and Mineral Resource Board (YGSMRB), the origin and age of such extrusive bodies that manifest on the surface as dikes, lava flows, and small (currently passive) cinder-cone volcanoes are of Cenozoic age associated with the rifting episode of the Arabian Peninsula and subsequent opening of the Red Sea. The overall aerial extension of the …

Water Flow Net Characterization By Using A Tank Model: Preliminary Outcome, Jasmin Budhan, Nazrul I. Khandaker, Stanley Schleifer

Publications and Research

A model study was conducted to observe and characterize the flow of water through sandy soil. One of the most relevant tools used for characterizing groundwater flow is the flow net. Assuming that water is incompressible and there is zero volume change in the soil mass, it is known that the total rate of inflow is to equal the total rate of outflow. Thus, following the principle of flow continuity, we use the Laplace equation of continuity, to observe the concept of the flow net. Computing the flow through a miniature channel, we observed the total head difference from the …

Nasa Maa (Murep Aerospace Academy) Stem Project At York College: Ensuring Future Stem Pipeline, Nazrul I. Khandaker, Shuayb Siddique, Matthew Khargie, Brandon Dhanraj, Zachary A. Sanichar, Mildred M. Selby, Chabenauth Ramnauth, Theresa Deepan, Yougeeta Singh, Krishna Mahabir, Sashi Singh, Omadevi Singh

Publications and Research

Our ongoing K1-12 NASA-supported STEM activities has served over 5000 children since 2015, largely from groups that are undeserved and underrepresented in the sciences. These STEM activities have been successfully delivered for several years and include earth science, meteorite geology, rocketry, aerodynamics, star gazing, EV3 Mindstorm robotics, basic coding exercises, wind tunnel, 3D-printing, etc., conducted largely through our present MAA (MUREP Aerospace Academy) Project. Corporate funding from the Con Edison and National Grid ensures additional STEM dissemination to the students during the summer operation. Significant positive component of the MAA program is the availability and willingness of the former student …

Recruiting And Retaining K9–16 Students Through Field- And Laboratory - Based Geoscience Experiences, Nazrul I. Khandaker, Stanley Schleifer, Arif M. Sikder, Krishna Mahabir, Ality Aghedo, Charren Cabaroy, Mildred M. Selby, Gugu Ginindza, Leonardo Sanchez

Publications and Research

Since 2004, we have been directly involved with the GSA to provide access and opportunities for K9-16 students, particularly those interested in the broader aspects of geoscience-related topics, to present their field-and- laboratory based research outcomes at professional conferences and to learn from each other. So far, well-over 400 students from the U. S. and abroad have taken advantage of this opportunity and participated our topical sessions. It is quite gratifying to report that many of these students, as a result of their attendance at the GSA conference, felt a continuing need for exposure to high-level professional venues with effective …

The Challenges Of Geotechnical Exploration In Bangladesh For Sustainable Urban Development And Risk Reductions In Engineering Geology, Mir Fazul Karim, Nazrul I. Khandaker, Muhammad Qumrul Hasson, A.T.M. Shakhawat Hossain

Publications and Research

Bangladesh is a unique example of rapid urbanization where the urban population increased from 5 to 58 million in last four decades. Due to complex geology and active tectonic setting, the urban ground is impacted by fluvio-deltaic processes and regional seismicity. The densely populated cities of the country are facing risks from many natural hazards like floods, tidal surge, riverbank and coastal erosion, scour, landslides, soil collapse and foundation failures. Geologists anticipate severe seismic threats from yet-undefined tectonic structures and seek to determine their consequential geo-structural responses and conformance to the national building code. With rapid growth, demands on infrastructure …

Evidence For Maxwell's Equations, Fields, Force Laws And Alternative Theories Of Classical Electrodynamics, Max Tran

Publications and Research

The set of equations known today as Maxwell's equations along with a few constitutive equations lie at the heart of classical electromagnetism. A common misconception held by many is that Maxwell's equations are essential, and that classical electromagnetic theory is settled science and is no longer an active field of investigations. We will review the four Maxwell's equations and related equations, their supporting experimental evidence, the field concept, and the Lorentz and Ritz force laws. We will give a brief outline of two approaches to classical electromagnetism which bypass Maxwell's equations, the propagated potential approach and the direct action approach …

Brownsfields To Greenfields: Environmental Justice Versus Environmental Gentrification, Juliana A. Maantay, Andrew Maroko

Publications and Research

Gentrification is a growing concern in many urban areas, due to the potential for displacement of lower-income and other vulnerable populations. This process can be accelerated when neighborhood “greening” projects are undertaken via governmental or private investor efforts, resulting in a phenomenon termed environmental or “green” gentrification. Vacant land in lower-income areas is often improved by the existing community through the creation of community gardens, but this contributes to these greening efforts and paradoxically may spur gentrification and subsequent displacement of the gardens’ stewards and neighbors. “Is proximity to community gardens in less affluent neighborhoods associated with an increased likelihood …

Brownfields To Greenfields: Environmental Justice Versus Environmental Gentrification, Juliana A. Maantay

Publications and Research

Gentrification is a growing concern in many urban areas, due to the potential for displacement of lower-income and other vulnerable populations. This process can be accelerated when neighborhood “greening” projects are undertaken via governmental or private investor efforts, resulting in a phenomenon termed environmental or “green” gentrification. Vacant land in lower-income areas is often improved by the existing community through the creation of community gardens, but this contributes to these greening efforts and paradoxically may spur gentrification and subsequent displacement of the gardens’ stewards and neighbors. “Is proximity to community gardens in less affluent neighborhoods associated with an increased likelihood …

Study Of The Kinetic Energy Densities Of Electrons As Applied To Quantum Dots In A Magnetic Field, Marlina Slamet, Viraht Sahni

Publications and Research

There are three expressions for the kinetic energy density t(r) expressed in terms of its quantal source, the single‐particle density matrix: t_A(r), the integrand of the kinetic energy expectation value; t_B(r), the trace of the kinetic energy tensor; t_C(r), a virial form in terms of the 'classical' kinetic field. These kinetic energy densities are studied by application to 'artificial atoms' or quantum dots in a magnetic field in a ground and excited singlet state. A comparison with the densities for natural atoms and molecules in their ground state is made. The near nucleus …

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 …

Character Sums Of Lee And Weintraub, Brad Isaacson

Publications and Research

We prove two conjectures of Lee and Weintraub and one conjecture of Ibukiyama and Kaneko about character sums arising as fixed point contributions in the Atiyah–Singer holomorphic Lefshetz formula applied to finite group actions on the space of certain Siegel cusp forms.

A Tool For Optimizing Java 8 Stream Software Via Automated Refactoring, Raffi T. Khatchadourian, Yiming Tang, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

Streaming APIs are pervasive in mainstream Object-Oriented languages. For example, the Java 8 Stream API allows for functional-like, MapReduce-style operations in processing both finite and infinite data structures. However, using this API efficiently involves subtle considerations like determining when it is best for stream operations to run in parallel, when running operations in parallel can be less efficient, and when it is safe to run in parallel due to possible lambda expression side-effects. In this paper, we describe the engineering aspects of an open source automated refactoring tool called Optimize Streams that assists developers in writing optimal stream software in …

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 …

Observed Differences Between Near-Surface Air And Skin Temperatures Using Satellite And Ground-Based Data, Satya Prakash, Farjana Shati, Hamidreza Norouzi, Reginald Blake

Publications and Research

Accurate estimates of long-term land surface temperature (T_s) and near-surface air temperature (T_a) at finer spatio-temporal resolutions are crucial for surface energy budget studies, for environmental applications, for land surface model data assimilation, and for climate change assessment and its associated impacts. The Atmospheric Infrared Sounder (AIRS) and Moderate Resolution Imaging Spectroradiometer (MODIS) sensors onboard the Aqua satellite provide a unique opportunity to estimate both temperatures twice daily at the global scale. In this study, differences between T_a and T_s were assessed locally over regions of North America from 2009 to 2013 …

The Diverse Magneto-Optical Selection Rules In Bilayer Black Phosphorus, Jhao-Ying Wu, Szu-Chao Chen, Thi-Nga Do, Wu-Pei Su, Godfrey Gumbs, Ming-Fa Lin

Publications and Research

The magneto-optical properties of bilayer phosphorene is investigated by the generalized tight-binding model and the gradient approximation. The vertical inter-Landau-level transitions, being sensitive to the polarization directions, are mainly determined by the spatial symmetries of sub-envelope functions on the distinct sublattices. The anisotropic excitations strongly depend on the electric and magnetic fields. A uniform perpendicular electric field could greatly diversify the selection rule, frequency, intensity, number and form of symmetric absorption peaks. Specifically, the unusual magneto-optical properties appear beyond the critical field as a result of two subgroups of Landau levels with the main and side modes. The rich and …