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Articles 1 - 30 of 38
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Historical Ozone Isopleths For Salt Lake Valley, Ut, Usa, Callum Flowerday, Isaac Sudweeks, Brad Adams, Jaron C. Hansen
Historical Ozone Isopleths For Salt Lake Valley, Ut, Usa, Callum Flowerday, Isaac Sudweeks, Brad Adams, Jaron C. Hansen
ScholarsArchive Data
EPA quality assured data, collected by the Utah Division of Air Quality, was used for this analysis.
Historical Analysis Of Urban Dust Generated By The Great Salt Lake Playa, Callum Flowerday, Jaron C. Hansen, Rebekah Stanley, Kaitlyn Brewster
Historical Analysis Of Urban Dust Generated By The Great Salt Lake Playa, Callum Flowerday, Jaron C. Hansen, Rebekah Stanley, Kaitlyn Brewster
ScholarsArchive Data
Historical PM10 filters, provided by the Utah Division of Air Quality, were analyzed for elemental composition of various metals. This was done using ICP-MS.
Also included, EPA PM10 historical data and bathymetry data provided by the Utah USGS.
Source Data For "Flowering Of Developable 2d Crystal Shapes In Closed, Fluid Membranes", Hao Wan, Geunwoong Jeon, Weiyue Xin, Gregory M. Grason, Maria M. Santore
Source Data For "Flowering Of Developable 2d Crystal Shapes In Closed, Fluid Membranes", Hao Wan, Geunwoong Jeon, Weiyue Xin, Gregory M. Grason, Maria M. Santore
Data and Datasets
Source data for "Flowering of Developable 2D Crystal Shapes in Closed, Fluid Membranes".
Quantitative Raman Analysis Of Human Blood Serum Of Glaucoma Patients Supplemented With Macular Pigment Carotenoids., Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh J. Byrne
Quantitative Raman Analysis Of Human Blood Serum Of Glaucoma Patients Supplemented With Macular Pigment Carotenoids., Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh J. Byrne
Datasets
Carotenoids have been widely studied for their high dietary, antioxidant, and vision protection roles in the human body. Blood contains all major dietary carotenoids and hence presents as a suitable and efficient substrate for the estimation of dietary carotenoids in vivo. Following the 18-month supplementation of open angle glaucoma patients with macula pigment carotenoids (Lutein, Zeaxanthin and Meso-Zeaxanthin) in the European Nutrition in Glaucoma Management (ENIGMA) trial, Raman spectroscopic analysis of the pre-supplementation baseline and 18-month supplemented blood serum carotenoids from participants was carried out, to investigate the systemic impact of supplementation in the blood and explore a more direct …
Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras
Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras
Faculty Publications
Air quality has important climate and health effects. There is a need, therefore, to monitor air quality both indoors and outdoors. Methods of measuring air quality should be cost-effective if they are to be used widely, and one such method is low-cost sensors (LCS). This study reports on the use of LCSs in Ulaanbataar, Mongolia to measure PM2.5 concentrations inside yurts or “gers”. Some of these gers were part of a non-government agency (NGO) initiative to improve insulating properties of these housing structures. The goal of the NGO was to decrease particulate emissions inside the gers; a secondary result …
Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) Coupled With An Interferometer For On-Band And Off-Band Detection Of Glyoxal, Callum Flowerday, Jaron Hansen, Ryan Thalman
Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) Coupled With An Interferometer For On-Band And Off-Band Detection Of Glyoxal, Callum Flowerday, Jaron Hansen, Ryan Thalman
ScholarsArchive Data
These data are the raw data from the BBCEAS. The "data_" files are the PMT data and the "DualDetection_08_02_2023" files are the spectrograph data. The PMT data are found in column 7 of the sheet. Column 1 is the time stamp.
Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody
Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody
ScholarsArchive Data
This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of Batch 1 1TEL-AA-vWa (SUMO) The solved structure used frames 1-999 and has been deposited in the wwPDB under the PDB ID 7N1O. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.
Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody
Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody
ScholarsArchive Data
This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of 3TEL-hlx-DARPin (SUMO) The solved structure used frames 1-1799 and has been deposited in the wwPDB under the PDB ID 7N2B. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.
Datadescription-Detection Of Sulfur Dioxide By Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas), Ryan Thalman, Nitish Bhardwaj, Callum Flowerday, Jaron C. Hansen
Datadescription-Detection Of Sulfur Dioxide By Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas), Ryan Thalman, Nitish Bhardwaj, Callum Flowerday, Jaron C. Hansen
ScholarsArchive Data
Files archived include the following:
Figure1.txt This file contains all the data used to make Figure 1 in the paper.
Figure4.txt This file contains all the data used to make Figure 4 in the paper.
Figure5.txt This file contains all the data used to make Figure 5 in the paper.
Figure6.txt This file contains all the data used to make Figure 6 in the paper.
Figure7.txt This file contains the code, written in Igor, that was used to generate this figure.
Figure8.txt This file contains all the data used to make Figure 8 in the paper.
Figure9.txt This file contains …
Loren Haarsma - When Did Sin Begin?, Loren Haarsma
Loren Haarsma - When Did Sin Begin?, Loren Haarsma
University Faculty Publications and Creative Works
Patrick Hamilton speaks to Calvin University Professor, Loren Haarsma, about the origins of sin and various ways to make sense of the doctrine of original sin in light of evolutionary origins. Other topics of conversation include psychology, free will and the theology of Saint Augustine.
Reeling In New Antibiotics: Synthesis And Antimicrobial Susceptibility Testing Of Zinc-Binding Clavanins From Styela Clava (Sea Squirt), Eduardo Badillo-Colberg
Reeling In New Antibiotics: Synthesis And Antimicrobial Susceptibility Testing Of Zinc-Binding Clavanins From Styela Clava (Sea Squirt), Eduardo Badillo-Colberg
Honors Scholar Theses
Clavanins have been a quite rarely studied antimicrobial peptide (AMP) family. Though the data in the few studies published on the matter and in theoretical experimental data presented by the Wang lab in their peptide library creation [14], in that the members of this family could potentially be quite effective novel antimicrobial candidates. Among those that have been targets of studies, Clavanin A has been at the forefront of this endeavor of finding effective novel antimicrobial peptides[14]. In these aforementioned studies, Clavanin A has been shown to be quite effective against many different bacterial strains, which begs the question as …
Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson
Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson
Research Data
This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig. This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp. The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis. In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect …
Audiobook Of A World From Dust, Ben Mcfarland
Audiobook Of A World From Dust, Ben Mcfarland
Faculty Open Access Books
A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.
It’s about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.
It’s about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.
It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and …
Four Hapten Spacer Sites Modulating Class Specificity: Nondirectional Multianalyte Immunoassay For 31 Β-Agonists And Analogues., Lanteng Wang, Wenmeng Jiang, Xing Shen, Xiangmei Li, Xin-An Huang, Zhenlin Xu, Yuanming Sun, Shun-Wan Chan, Lingwen Zeng, Eremin Sergei Alexandrovich, Hongtao Lei
Four Hapten Spacer Sites Modulating Class Specificity: Nondirectional Multianalyte Immunoassay For 31 Β-Agonists And Analogues., Lanteng Wang, Wenmeng Jiang, Xing Shen, Xiangmei Li, Xin-An Huang, Zhenlin Xu, Yuanming Sun, Shun-Wan Chan, Lingwen Zeng, Eremin Sergei Alexandrovich, Hongtao Lei
Faculty of Science & Technology (THEi)
Immunoassay methods are important for monitoring β-agonists illegally used for reducing animal fat deposition in livestock. However, there is no simultaneous screening surveillance immunoassay for detecting various β-agonist chemicals that are possibly present in food. In this study, through the use of an R-(−)-salbutamol derivative as the immunizing hapten, an antibody recognizing 31 β-agonists and analogues was generated for the first time. Three-dimensional quantitative structure–activity relationship (3D QSAR) revealed that strong steric and hydrophobic fields around the hapten spacer near C-2, as well as a chirality at C-1′, dominantly modulated the class specificity of the raised antibody. However, a hapten …
Biochemistry Lecture Notes, Chavonda Mills, Shaundra Walker
Biochemistry Lecture Notes, Chavonda Mills, Shaundra Walker
Chemistry Ancillary Materials
The following set of lecture notes are ancillary materials for Oregon State University's Biochemistry: Free for All.
This ancillary set was created under a Round Five ALG Textbook Transformation Grant. They are also available in an open-course format through LibGuides:
http://libguides.gcsu.edu/millsbiochem3510
Susceptibility Of Chlamydia Trachomatis To The Excipient Hydroxy-Ethylcellulose: Ph And Concentration Dependence Of Antimicrobial Activity, Ali A. Abdul-Sater, David M. Ojcius, M. P. Meyer
Susceptibility Of Chlamydia Trachomatis To The Excipient Hydroxy-Ethylcellulose: Ph And Concentration Dependence Of Antimicrobial Activity, Ali A. Abdul-Sater, David M. Ojcius, M. P. Meyer
David M. Ojcius
Hydroxyethyl cellulose (HEC) is used as a neutral excipient in microbicides used against sexually transmitted pathogens. However, HEC inhibits the infection of cervical epithelial cells by Chlamydia trachomatis at pH 5 in a concentration-dependent manner. At pH 7, infection is inversely dependent on the concentration of HEC, possibly due to pH-dependent calcium sequestration.
Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron
Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron
Statistical Sciences and Operations Research Data
This zip file contains Matlab scripts and ode (XPP) files to calculate the statistics of the models in "Noise-Enhanced Coding in Phasic Neuron Spike Trains". This article is published in PLoS ONE.
A Study Of Defensive Mechanisms Employed By Two Species Of Nudibranchs Using Toxicity And Unpalatability Analyses, Sean Youn
Independent Study Project (ISP) Collection
Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays were used …
Force Generation And Contraction Of Random Actomyosin Bundles., Dietmar B. Oelz
Force Generation And Contraction Of Random Actomyosin Bundles., Dietmar B. Oelz
Biology and Medicine Through Mathematics Conference
No abstract provided.
2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin
2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin
Bioinformatics Software Design Projects
Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.
Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …
O-Glcnacylation And Modifications To The Class Ii Transactivator, Ronald Shanderson
O-Glcnacylation And Modifications To The Class Ii Transactivator, Ronald Shanderson
Georgia State Undergraduate Research Conference
No abstract provided.
Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries
Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries
USF Tampa Graduate Theses and Dissertations
The vast variety of long-chain fatty acid amides identified in biological systems is intriguing. The general structure of a fatty acid amide is R-CO-NH-X, where R is an alkyl group and X is derived from an immense variety of biogenic amines. Although structurally simple, the bioactivities of these molecules as signaling lipids are very diverse and have just recently begun to emerge in the literature. Interest in the long-chain fatty acid amides dramatically increased following the identification and characterization of one specific N-acylethanolamine, N-arachidonoylethanolamine (anandamide), as the endogenous ligand for the cannabinoid receptors in the mammalian brain. Since …
Stellaris Fishing 20131125mon Part 1 Of 2, George Mcnamara
Stellaris Fishing 20131125mon Part 1 Of 2, George Mcnamara
George McNamara
Stellaris FISH dataset using three FISH probe sets. Slides courtesy of Biosearch Technologies,
https://www.biosearchtech.com/store/product.aspx?catid=224,318,324
see http://stellarisfish.smugmug.com/ for online gallery by Biosearch.
This experiment was to evaluate the crosstalk between the Biosearch fluorophores:
Quasar 570
CAL Fluor Red 610 (CFR 610)
Quasar 670
DAPI (DNA counterstain)
Autofluorescence (green, but sometimes showing up in other channels).
and our lab's Leica DMI6000 fluorescence microscope with Leica filter sets:
DAPI
GFP (L5)
Cy3 (N3)
Texas Red (TxRed2)
Cy5 (Y5)
I also acquired green channel and red channel with exciter filters in our ASI excitation wheel:
GFP + 492 exciter
Texas Red (TxRed2) + 572 …
Stellaris Fishing 20131125mon Part 2 Of 2, George Mcnamara
Stellaris Fishing 20131125mon Part 2 Of 2, George Mcnamara
George McNamara
Stellaris FISH dataset using three FISH probe sets.
Slides courtesy of Biosearch Technologies,
https://www.biosearchtech.com/store/product.aspx?catid=224,318,324
see http://stellarisfish.smugmug.com/ for online gallery by Biosearch.
This experiment was to evaluate the crosstalk between the Biosearch fluorophores:
Quasar 570
CAL Fluor Red 610 (CFR 610)
Quasar 670
DAPI (DNA counterstain)
Autofluorescence (green, but sometimes showing up in other channels).
and our lab's Leica DMI6000 fluorescence microscope with Leica filter sets:
DAPI
GFP (L5)
Cy3 (N3)
Texas Red (TxRed2)
Cy5 (Y5)
I also acquired green channel and red channel with exciter filters in our ASI excitation wheel:
GFP + 492 exciter
Texas Red (TxRed2) + 572 …
Helix Turn Helix Domain, David J. Hall
Helix Turn Helix Domain, David J. Hall
Protein Domains
Helix turn helix domain #3V1A. The helix-turn helix is a DNA-binding domain. The two alpha helices are the reading or recognition helices, which bind in a groove in the DNA and recognize specific gene regulatory sequences in the DNA.
Ring Domain, David J. Hall
Ring Domain, David J. Hall
Protein Domains
Ring domain #1CHC. The RING finger is a specialized type of Zn finger consisting of 40–60 residues that binds two atoms of zinc, and is involved in mediating protein—protein interactions. Many zinc fingers bind nucleic acids. The presence of a RING finger domain is a characteristic of RING-class E3 ubiquitin protein ligases capable of transferring ubiquitin from an E2 enzyme to a substrate protein.
Sh2 Domain, David J. Hall
Sh2 Domain, David J. Hall
Protein Domains
SH2 domain #1BFJ. Src-homology 2 (SH2) domains are modules of ~100 amino acids that bind to specific phospho tyrosine (pY) containing peptide motifs. Conventional SH2 domains have a conserved pocket that recognizes pY, and a more variable pocket that binds 3-6 residues C-terminal to the pY and confers specificity.
Sh3 Domain, David J. Hall
Sh3 Domain, David J. Hall
Protein Domains
SH3 domain #1NEB. Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.
Ig Domain, David J. Hall
Ig Domain, David J. Hall
Protein Domains
Ig domain #2CKN. This particular domain is named for the first protein in which it was found, the immunoglobulin. An immunoglobulin is a antibody. Antibodies are generated by our immune system to recognize the specific size, shape and charge of pathogens. This domain is also found on the extracellular portion of many receptors including the interleukin-1 family of receptors.
Beta Barrel, David J. Hall
Beta Barrel, David J. Hall
Protein Domains
Beta barrel (cyan fluorescent protein) #4AR7. This fluorescent protein is a variation of green fluorescent protein from a jellyfish and is the only domain that is a complete protein. The protein is routinely used to visualize a variety of biological processes. The beta barrel domain is a beta sheet wrapped around the fluorescent active site to provide structure.