Digital Commons Network^™

Reading Effectively Across The Disciplines (Read): A Strategy To Improve Student Success, Juanita But, Pamela Brown, Davida Smyth

Publications and Research

This paper describes the structure and activities of READ (Reading Effectively Across the Disciplines), a pilot initiative to improve students’ critical reading skills, disciplinary literacy and academic success. READ employs a multimodal design that consists of faculty training in disciplinary literacy instruction and curricular enhancement, development and implementation of active reading assignments and assessments, peer-led team learning, and the dissemination of discipline-specific teaching and learning resources on an Open Lab site to provide an interactive teaching and learning environment for students and faculty. Empirical evidence of the initial effectiveness of the pilot in three gateway courses in Biology, Electromechanical Engineering …

Polyphenols Content And Antioxidant Activity Of Artemisia Sieversiana Willd. In Western Pamir, Gulazor Miravalova, Sh. Kurbonbekova, Sh. Satorov, Akobir Mirzorahimov, Dovudsho Navruzshoev, Vyacheslav Dushenkov, M. Vakhidova

Publications and Research

Polyphenols content and antioxidant activity in Artemisia sieversiana Willd. were investigated in relation to the altitude of the plant growth in the Western Pamir region. Antioxidant activity generally correlated with the polyphenols content. However, no significant association was found between an altitude of the sample collection and polyphenols content or antioxidant activity.

'Civil Wars: A History In Ideas' By David Armitage (Review), Zachary C. Shirkey

Publications and Research

No abstract provided.

Dismantling Motivational Interviewing: Effects On Initiation Of Behavior Change Among Problem Drinkers Seeking Treatment, Jon Morgenstern, Alexis Kuerbis, Jessica Houser, Sijing Shao, James R. Mckay

Publications and Research

Motivational Interviewing (MI) is an efficacious treatment for alcohol use disorders (AUD). MI is thought to enhance motivation via a combination of two therapeutic strategies or active ingredients: one relational and one directional. The primary aim of this study was to examine MI’s hypothesized active ingredients using a dismantling design. Problem drinkers (N=139) seeking treatment were randomized to one of three conditions: MI, relational MI without the directional elements labeled spirit-only MI (SOMI) or a non-therapy control (NTC) condition and followed for eight weeks. Those assigned to MI or SOMI received four sessions of treatment over eight weeks. All participants …

A Pilot Study Of Online Feedback For Adult Drinkers 50 And Older: Feasibility, Efficacy, And Preferences For Intervention, Alexis Kuerbis, Lisa Hail, Alison A. Moore, Frederick Muench

Publications and Research

Normative (NF) and personalized feedback (PF) are moderately effective brief interventions for at-risk drinking middle-aged and older adults. This study tested the feasibility of online feedback for drinkers 50 and older. This study’s aims were to identify whether there is differential effectiveness of PF over NF in prompting drinkers 50 years old and older to plan for change and to determine potential preferences for intervention among adult drinkers 50 and older with practical knowledge about computers. Method—Using Amazon’s Mechanical Turk, 138 male and female drinkers aged 50 to 75+ were recruited to complete an online survey that asked about their: …

Bioanalysis For Cocaine, Opiates, Methadone And Amphetamines Exposure Detection During Pregnancy, Marta Concheiro, Elena Lendoiro, Ana De Castro, Eva Gonzalez-Colmenero, Ana Concheiro-Guisan, Patricia Penas-Silva, Manuel Macias-Cortina, Angelines Cruz-Landeira, Manuel Lopez-Rivadulla

Publications and Research

Drug exposure during pregnancy constitutes a major legal issue and public health concern. Drug and metabolite determination in biological matrices from mother and newborn is an objective indication of prenatal drug exposure. However, limited data are available regarding the interpretation of these analytical results in terms of window of detection and degree of exposure. We collected paired maternal hair, meconium, placenta and umbilical cord from 727 mother-newborn dyads. We analyzed these specimens by liquid chromatography tandem mass spectrometry for the determination of cocaine, opioids, methadone and amphetamines, and compared the analytical results from the four different matrices. The cases were …

Vital Exhaustion, Burnout, And Other Avatars Of Depression, Bianchi Renzo, Irvin Sam Schonfeld, Eric Laurent

Publications and Research

In our view, there is a worrying tendency in psychology and medicine to let proliferate “depression-like” constructs—a transgression of the scientific canon of parsimony. The problem is not limited to vital exhaustion (VE). Burnout, a condition akin to VE, has been shown to problematically overlap with depression. Compassion fatigue, a condition that shows particularly blurred definitional contours, is also uncomfortably close to depressive symptomatology. The construct of neurasthenia may be part of this confusing trend as well, although neurasthenia has been elevated to the status of nosological category in the ICD. Construct proliferation jeopardizes knowledge growth by undermining theory building …

Biological Research On Burnout-Depression Overlap: Long-Standing Limitations And On-Going Reflections, Renzo Bianchi, Irvin Sam Schonfeld, Eric Laurent

Publications and Research

In this commentary, we discuss seldom-noticed methodological problems affecting biological research on burnout and depression and make recommendations to overcome the limitations of past studies conducted in this area. First, we suggest that identified subtypes of depression (e.g., depression with melancholic features and depression with atypical features) should be taken into account in future biological research on burnout and depression, given that different subtypes of depression have been associated with distinct autonomic and neuroendocrine profiles. Second, we underline that research on burnout-depression overlap is made difficult by the absence of a consensual conceptualization and operationalization of burnout. In order to …

Testing Cross-Sectional And Prospective Mediators Of Internalized Heterosexism On Heavy Drinking, Alcohol Problems, And Psychological Distress Among Heavy Drinking Men Who Have Sex With Men, Alexis Kuerbis, Ethan Mereish, Marie Hayes, Christine Davis, Sijing Shao, Jon Morgenstern

Publications and Research

Objective: Minority stress theory is often used as a causal explanation for substance use among lesbian, gay, and bisexual populations. This study tested whether drinking to cope with stress (DTC), loneliness, and gay community participation (GCP) mediated the relationship between one type of minority stress (i.e., internalized heterosexism, IH) and behavioral health outcomes. Method: Utilizing secondary data analysis and the PROCESS procedure, relationships between IH, the mediators (DTC, loneliness, and GCP), and outcomes (heavy drinking, alcohol problems, and psychological distress) were explored, both cross-sectionally and in a lagged manner, among both treatment seeking and non-treatment seeking problem drinking men who …

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

Lemurfaceid: A Face Recognition System To Facilitate Individual Identification Of Lemurs, David Crouse, Rachel L. Jacobs, Zach Richardson, Scott Klum, Anil Jain, Andrea L. Baden, Stacey R. Tecot

Publications and Research

Background: Long-term research of known individuals is critical for understanding the demographic and evolutionary processes that influence natural populations. Current methods for individual identification of many animals include capture and tagging techniques and/or researcher knowledge of natural variation in individual phenotypes. These methods can be costly, time-consuming, and may be impractical for larger-scale, populationlevel studies. Accordingly, for many animal lineages, long-term research projects are often limited to only a few taxa. Lemurs, a mammalian lineage endemic to Madagascar, are no exception. Long-term data needed to address evolutionary questions are lacking for many species. This is, at least in part, due …

Rapidly Deployed And Assembled Tensegrity System: An Augmented Design Approach, Phillip Anzalone, Stephanie Bayard, Ralph S. Steenblik

Publications and Research

The Rapidly Deployable and Assembled Tensegrity (RDAT) project enables the efficient automated design and deployment of differential-geometry tensegrity structures through computation-driven design-to-installation workflow. RDAT employs the integration of parametric and solid-modeling methods with production by streamlining computer numerically controlled manufacturing through novel detailing and production techniques to develop an efficient manufacturing and assembly system. The RDAT project emerges from the Authors' research in academia and professional practice focusing on computationally produced full-scale performative building systems and their innovative uses in the building and construction industry.

Burnout And The Hypothalamic-Pituitary-Thyroid Axis: A Methodological Comment, Renzo Bianchi, Irvin Sam Schonfeld, Eric Laurent

Publications and Research

Because (a) burnout overlaps with depression and (b) depression has been associated with altered functioning of the hypothalamic-pituitary-thyroid axis changes in the activity of the HPT axis can be expected in burnout. Most probably, Guo et al.’s (2017) results are flawed by a severe form of the “healthy worker effect.”

Optimal Use Of Eeg Recordings To Target Active Brain Areas With Transcranial Electrical Stimulation, Jacek P. Dmochowski

Publications and Research

To demonstrate causal relationships between brain and behavior, investigators would like to guide brain stimulationusing measurements of neural activity. Particularly promising in this context are electroencephalography (EEG) and transcranial electrical stimulation (TES), as they are linked by a reciprocity principle which, despite being known for decades, has not led to a formalism for relating EEG recordings to optimal stimulation parameters. Here we derive a closed-form expression for the TES configuration that optimally stimulates (i.e., targets) the sources of recorded EEG, without making assumptions about source location or distribution. We also derive a duality between TES targeting and EEG source …

Borneol, A Novel Agent That Improves Central Nervous System Drug Delivery By Enhancing Blood–Brain Barrier Permeability, Qun-Lin Zhang, Bingmei M. Fu, Zhang-Jin Zhang

Publications and Research

The clinical application of central nervous system (CNS) drugs is limited by their poor bioavailability due to the blood–brain barrier (BBB). Borneol is a naturally occurring compound in a class of ‘orificeopening’ agents often used for resuscitative purposes in traditional Chinese medicine. A growing body of evidence confirms that the ‘orifice-opening’ effect of borneol is principally derived from opening the BBB. Borneol is therefore believed to be an effective adjuvant that can improve drug delivery to the brain. The purpose of this paper is to provide a comprehensive review of information accumulated over the past two decades on borneol’s chemical …

The Impact Of New York State's 2016 Mold Licensing Requirement On Indoor Air Quality Assessments, Angelo Lampousis, Mark Drozdov

Publications and Research

As of January 2016, New York joined a select number of states in regulating mold. The New York State Department of Labor has approved mold-related training courses in three levels, ranging from two to four days. These include the mold abatement worker, mold remediation contractor, and mold assessor courses. In this presentation we share the experience obtained to date from delivering the above referenced courses and challenges as an approved training provider. We also evaluate the relative effectiveness of the mode of delivery as it relates to different audiences.

T. E. Lawrence's Seven Pillars Of Wisdom And The Erotics Of Literary History: Straddling Epic., Václav Paris

Publications and Research

No abstract provided.

Dynamical Systems Modeling To Identify A Cohort Of Problem Drinkers With Similar Mechanisms Of Behavior Change, Kidist Maxwell, Rebecca Everett, Sijing Shao, Alexis Kuerbis, Lyric Stephenson, H. T. Banks, Jon Morgenstern

Publications and Research

One challenge to understanding mechanisms of behavior change (MOBC) completely among individuals with alcohol use disorder is that processes of change are theorized to be complex, dynamic (time varying), and at times non-linear, and they interact with each other to influence alcohol consumption. We used dynamical systems modeling to better understand MOBC within a cohort of problem drinkers undergoing treatment. We fit a mathematical model to ecological momentary assessment data from individual patients who successfully reduced their drinking by the end of the treatment. The model solutions agreed with the trend of the data reasonably well, suggesting the cohort patients …

The Replication Initiator Of The Cholera Pathogen’S Second Chromosome Shows Structural Similarity To Plasmid Initiators, Natalia Orlova, Matthew Gerding, Olha Ivashkiv, Paul Dominic B. Olinares, Brian T. Chait, Matthew K. Waldor, David Jeruzalmi

Publications and Research

The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a headto- head dimeric configuration …

Bioremoval Of Phenol From Aqueous Solutions Using Native Caribbean Seaweed, Abel E. Navarro, Anibal Hernandez-Vega, Md Emran Masud, Loretta M. Roberson, Liz M. Diaz-Vázquez

Publications and Research

Among several Puerto Rican algae, Sargassum sp. (SG) and Chaetomorpha (CM) showed the highest phenol adsorption capacity from aqueous solutions and were used in optimized adsorption batch experiments at room temperature. The effects of pH, adsorbent dose, phenol concentration, salinity and presence of interfering substances were evaluated. Initial solution pH exhibited a strong effect, mainly on the phenol aqueous chemistry; showing the maximum adsorption at pH 10. Sorption isotherm results were modelled according to the Langmuir, Tempkin and Freundlich equations. Isotherm modelling indicated a maximum adsorption capacity (qmax) of 82.10 and 17.7 mg of phenol per gram of SG and …

A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents

Publications and Research

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …

Liver Enzymes And Risk Of Ischemic Heart Disease And Type 2 Diabetes Mellitus: A Mendelian Randomization Study, Junxi Liu, Shiu Lun Au Yeung, Gabriel M. Leung, C. Mary Schooling

Publications and Research

We used Mendelian randomization to estimate the causal effects of the liver enzymes, alanine aminotransferase (ALT), alkaline phosphatase (ALP) and gamma glutamyltransferase (GGT), on diabetes and cardiovascular disease, using genetic variants predicting these liver enzymes at genome wide significance applied to extensively genotyped case-control studies of diabetes (DIAGRAM) and coronary artery disease (CAD)/myocardial infarction (MI) (CARDIoGRAMplusC4D 1000 Genomes). Genetically higher ALT was associated with higher risk of diabetes, odds ratio (OR) 2.99 per 100% change in concentration (95% confidence interval (CI) 1.62 to 5.52) but ALP OR 0.92 (95% CI 0.71 to 1.19) and GGT OR 0.88 (95% CI 0.75 …

A Mineralized Alga And Acritarch Dominated Microbiota From The Tully Formation (Givetian) Of Pennsylvania, Usa, John A. Chamberlain Jr., Rebecca B. Chamberlain, James O. Brown

Publications and Research

Sphaeromorphic algal cysts, most probably of the prasinophyte Tasmanites, and acanthomorphic acritarch vesicles, most probably Solisphaeridium, occur in a single 20 cm thick bed of micritic limestone in the lower part of the Middle Devonian (Givetian) Tully Formation near Lock Haven, Pennsylvania. Specimens are composed of authigenic calcite and pyrite crystals about 5–10 µm in length. Some specimens are completely calcitic; some contain both pyrite and calcite; and many are composed totally of pyrite. The microfossils are about 80 to 150 µm in diameter. Many show signs of originally containing a flexible wall composed of at least two layers. Some …

The Vibrio Cholerae Minor Pilin Tcpb Initiates Assembly And Retraction Of The Toxin- Coregulated Pilus, Dixon Ng, Tony Harn, Tuba Altindal, Subramania Kolappan, Jarrad M. Marles, Rajan Lala, Ingrid Spielman, Yang Gao, Caitlyn A. Hauke, Gabriela Kovacikova, Zia Verjee, Ronald K. Taylor, Nicolas Biais, Lisa Craig

Publications and Research

Type IV pilus (T4P) systems are complex molecular machines that polymerize major pilin proteins into thin filaments displayed on bacterial surfaces. Pilus functions require rapid extension and depolymerization of the pilus, powered by the assembly and retraction ATPases, respectively. A set of low abundance minor pilins influences pilus dynamics by unknown mechanisms. The Vibrio cholerae toxin-coregulated pilus (TCP) is among the simplest of the T4P systems, having a single minor pilin TcpB and lacking a retraction ATPase. Here we show that TcpB, like its homolog CofB, initiates pilus assembly. TcpB co-localizes with the pili but at extremely low levels, equivalent …

Improved Genome-Scale Multitarget Virtual Screening Via A Novel Collaborative Filtering Approach To Cold-Start Problem, Hansaim Lim, Paul Gray, Lei Xie, Aleksandar Poleksic

Publications and Research

Conventional one-drug-one-gene approach has been of limited success in modern drug discovery. Polypharmacology, which focuses on searching for multi-targeted drugs to perturb disease-causing networks instead of designing selective ligands to target individual proteins, has emerged as a new drug discovery paradigm. Although many methods for single-target virtual screening have been developed to improve the efficiency of drug discovery, few of these algorithms are designed for polypharmacology. Here, we present a novel theoretical framework and a corresponding algorithm for genome-scale multitarget virtual screening based on the one-class collaborative filtering technique. Our method overcomes the sparseness of the protein-chemical interaction data by …

Review Of The Cultivation Program Within The National Alliance For Advanced Biofuels And Bioproducts, Peter J. Lammers, Michael Huesemann, Wiebke Boeing, Daniel B. Anderson, Robert G. Arnold, Xuemei Bai, Manish Bhole, Yalini Brhanavan, Louis Brown, Jola Brown, Judith K. Brown, Stephen Chisholm, C. Meghan Downes, Scott Fulbright, Yufeng Ge, Jonathan E. Holladay, Balachandran Ketheesan, Avinash Khopkar, Ambica Koushik, Paul Laur, Babetta L. Marrone, John B. Mott, Nagamany Nirmalakhandan, Kimberly L. Ogden, Ronald L. Parsons, Juergen Polle, Randy D. Ryan, Tzachi Samocha, Richard T. Sayre, Mark Seger, Thinesh Selvaratnam, Ruixiu Sui, Alex Thomasson, Adrian Unc, Wayne Van Vorrhies, Peter Waller, Yao Yao, José A. Olivares

Publications and Research

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB)were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium test beds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive and …

Siddhartha Mukherjee. The Gene. An Intimate History. New York: Scribner, 2016. 593 Pp. $32.00 Cloth (Isbn 978-1-4767-3350-0), Aldemaro Romero Jr.

Publications and Research

Heredity has always been, in one form or another, at the center of biological

research. There is little doubt that the first scientific experimentation took place

about fifteen thousand years ago, when humans started breeding plants and

animals in order to domesticate them. Today the science of genetics seems to

advance at such a pace that even the experts have trouble keeping up with all the

developments. Now we are witnessing the expansion of our understanding of this

realm of science to levels unimaginable just a few decades ago.

Comparative Phylogeography In The Atlantic Forest And Brazilian Savannas: Pleistocene Fluctuations And Dispersal Shape Spatial Patterns In Two Bumblebees, Elaine Françoso, Alexander Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias

Publications and Research

Background: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results: Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that …

Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone

Publications and Research

Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement …

Efficient Method For Transfer Of Microinjected Eggs To Mouse Ampulla For Generating Transgenic Mice, Guang Wen, Jin Di, Qian Li, Jianling Chen, Ling Jin, Cheng Wang, Sanqing Xu

Publications and Research

Background: The new method described here is highly efficient in transferring microinjected mouse eggs (MEs) through the bursa membrane of a surrogate mother mouse to the ampulla of the oviduct without damaging the blood vessels on the bursa membrane.

Results: This method causes no loss of blood, and it produces newborn pups/founders from approximately 70% of the transferred MEs, because only a small hole is made on the blood vessel–free area of the bursa membrane and ampulla of the surrogate mother mouse. The infundibulum remains intact. The small hole on the bursa membrane/ ampulla may already heal up before the …