bluuebunny/crossref_metadata_2025_split huggingface dataset:
MATLAB Tool for Color Comparative Analysis in Fixed Specimens. A Five Solution Single Blind Controlled Trial
Authors: Mejia Gabriel Mateo , Pedraza Juan Daniel , Rueda-Esteban Roberto Javier 
Published: April 2020

Formaldehyde fixation avoids decomposition process of cadaveric specimens
1, making them useful for anatomy teaching and research
2. However, formaldehyde leads to fresh appearance loss in the tissue, which reduces its academical value. Although some color recovery solutions have been presented
3,
4, no standardized method for quantitative color assessment in fixed tissues has been proposed.Our aim of is to present a MATLAB tool for color recovery analysis in formaldehyde fixed tissues.Four different animal tissues (cardiac and skeletal muscle, kidney and liver), previously fixed with 10% formaldehyde (v/v) were treated in five different solutions (mineral staining, sodium bisulfite, sodium bicarbonate, GERDEX and modified Chilean solution
3). Tissues were photographed at different stages of preservation. Analysis was carried out in two different spaces of chromatic representation (RGB and HSV).A computerized color comparison tool was developed allowing visualization of the chromatic presence in RGB color space through a three‐dimensional distribution (color cloud). Besides color cloud intersection percentage, frequency histograms of RGB distributions and the color saturation (S) distribution were used to generate performance metrics based on the Bhattacharyya distance. Each metric addressed one specific desired characteristic of a color recuperated specimen.Mineral staining proved to be the solution with the best overall performance across most of the proposed metrics, significantly recovering the color compared to fresh tissue. Although significant results were obtained, future works implementing more robust methods of comparison, that involve metrics based on multiple desirable characteristics of a specimen are necessary.The MATLAB tool developed showed to be useful for the quantitative color analysis and comparison in formaldehyde fixed tissues. Further studies should be done to standardize quality metrics of existing and upcoming preservation techniques.Support or Funding InformationAnatomy Laboratory, School of Medicine, Universidad de los Andes.
Development of a gel filtration protocol that eliminates precipitation during refolding of chemically denatured proteins
Authors: Odunuga Odutayo , Tovar Carmel N. 
Published: April 2020

Purification of recombinant proteins in denaturing conditions has many practical advantages. Chemical denaturants such as urea and guanidine hydrochloride are used to solubilize recombinant proteins from inclusion bodies. Proteins purified in denaturing conditions generally contain fewer contaminants compared to their counterparts purified in native buffers; thus reducing the number of steps in the purification scheme. Chemically denatured proteins can be stored for long time in buffer containing the denaturant and then refolded as required. Refolding is commonly performed by equilibrium dialysis and sometimes on metal affinity columns by diluting out the denaturant and allowing the protein to fold back into its native state. The refolding steps often result in significant loss of protein through aggregation. Using a modified gel filtration technique, we successfully refolded a spectrum of proteins that either are highly aggregation‐prone or contain several disulfide bonds or both, back to their native states. Some of the proteins are well known to precipitate significantly during refolding. However, using this technique, precipitation was either minimal or non‐existent. Secondary and tertiary structural analyses coupled with functional assays confirmed that these proteins were correctly refolded and biologically active. This strategy provides a robust approach to refolding denatured proteins, and simultaneously performing buffer exchange and additional purification steps.Support or Funding InformationRobert A. Welch Foundation Grant #AN‐0008
Effects of ambient temperature on place conditioning elicited by abused psychostimulants in mice: role of methylexenedioxy moiety
Authors: Simmons Simeon , Russell Lauren , Fantegrossi William 
Published: April 2020

Preclinical studies of the pharmacological and toxicological effects of drugs of abuse only rarely mimic the settings in which these substances are used by humans. In the case of psychostimulant drugs, human users often administer these compounds in party or musical festival settings characterized by loud noise, crowding, and warm ambient temperature. Each of these environmental factors may impact numerous drug effects, including thermoregulation, locomotor stimulation and lethality. Our previous work with 3,4‐methylenedioxymethamphetamine (MDMA) and 3,4‐methylenedioxypyrovalerone (MDPV) suggests that the presence of a methylenedioxy ring moiety may be required for a given drug to display these environment‐dependent effects. In these studies, we were specifically interested in testing this hypothesis with regards to abuse‐related effects in mice. We used conditioned place preference to establish dose‐effect curves for apparent rewarding effects for two pairs of psychostimulant drugs which differ structurally only in the presence or absence of a methylenedioxy ring. We studied two amphetamine analogues (MDMA and methamphetamine) and two cathinone analogues (MDPV and α‐pyrrolidinopentiophenone [α‐PVP]) at both a cool (20°C) and a warm (28°C) ambient temperature. As expected, all four drugs elicited significant dose‐dependent place preference at the cool ambient temperature. Doses of MDMA and MDPV – which both contain methylenedioxy rings – which were devoid of place preference effects in the cool ambient temperature elicited significant preference at the warm ambient temperature. This was not the case for methamphetamine or α‐PVP – which both lack the methylenedioxy ring – as doses of both compounds which were ineffective at the cool temperature remained ineffective at the warm temperature. These studies suggest that abuse of psychostimulants containing a methylenedioxy ring may be potentiated by warm ambient temperatures, which are commonly found in the environments where they are typically used by humans. Furthermore, this suggests that preclinical abuse liability studies conducted at standard laboratory temperatures may underestimate the potency of psychostimulant drugs with a methylenedioxy moiety.Support or Funding InformationThese studies supported by an institutional ASPET SURF award (SS), T32 DA022981 (LNR) and R01 DA039195 (WEF).
Determining the Structure and Kinetics of Desferroxiamine D Variants: E445A and H443A
Authors: Rosales Vincent , Gahir Paven , Hoffmann Katherine 
Published: April 2020

Virulent bacteria such as MRSA and anthrax produce siderophores which are successful in competing for and chelating iron from their host environment. These are synthesized by a family of enzymes called NIS synthetases, of which DesD is a model enzyme out of Streptomyces coelicolor. DesD contributes to the catalytic formation of siderophore Desferrioxamine E, a siderophore formed by iterative combination of three molecules of hydroxysuccinylcadaverine along with stoichiometric amounts of cofactor ATP. We have previously characterized the kinetic constants for ATP and the largest substrate, called dfoG, as well as binding studies for the cofactors and analogs and structural models of the apo and analog‐bound enzyme. The purpose of the current study is to determine the sidechains involved in catalysis by using site directed mutagenesis, kinetic studies, binding studies and crystallography to analyse the impact of the mutation. This work will focus on two variants: E445A and H445A which we hypothesize will be critical for cofactor binding (E445A) and catalysis (H445A) based on alignments and structural analysis. The current work will present overexpression and purification of these two variants, along with the biochemical characterization of their functions.Support or Funding InformationThis research was supported in part by the National Science Foundation (NSF‐RUI grant 1716986 to K.M.H.).
PhUn Day: Third Times a Charm
Authors: Rascon Jozelyn A. , Trujillo Elizabeth , Aguilar Brianna C. , Guerrero Mariana , Keller Aaron A. , Rico Andrea A. , Nunez Victoria A. , Gurovich Alvaro 
Published: April 2020

Physiology Understanding (PhUn) week consists of hands‐on activities and presentations, which incorporate the understanding of physiology through interactive fun. The University of Texas at El Paso’s Rehabilitation Sciences Program has hosted PhUn week in different schools throughout the El Paso community for a total of three years. Our first year in 2017, PhUn week was hosted at Hornedo Middle School and the activity reached seventh‐grade students (24). The following year in 2018, PhUn week was hosted at Tippin Elementary School and its whole second grade (96 students) and teachers (5) participated in the event. Although the American Physiological Society is no longer sponsoring PhUn week, we did not want to let this great community outreach project come to an end. Therefore, this year (2019) PhUn “day” was hosted at Kohlberg Elementary School in El Paso, Texas with the participation of its entire third‐grade class (80 students) and teachers (5). Since many of the students in the Rehabilitation Sciences program have participated in PhUn week in the past, we received great support in planning the event. We split up into teams and designed 5 new and exciting stations using electronic physiology data acquisition systems. These stations included reaction time, electromyography, and a stroke simulation which was designed to immobilize one side of the body and challenge cognition. We also had a working heart model showing the circulation of blood, and a sensory integration station in which students learned how the brain receives information from the 5 senses, organizes this information and responds appropriately. We used the Biopac MP40 system to conduct the reaction time and EMG stations. Each group of volunteers had one leader who participated in the previous years who was able to train the other students in the use of the Biopac MP40 system. We split the 80 students into groups of 16 and had them rotate every 20 minutes. The students, teachers, and other Kohlberg faculty, as well as UTEP students, had a lot of fun and learned about physiology at the same time. We could see the excitement and effect the event left on the young students as many left excited about science, which is the main goal of PhUn week. Overall, it was a great experience that required a lot of preparation and training but was worth the impact it had on the students involved.Support or Funding InformationResearch reported in this poster was supported by the National Institute of General Medical Sciences of the National Institutes of Health under linked Award Numbers RL5GM118969, TL4GM118971, and UL1GM118970. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
PBK is a Novel Regulator of Vascular Remodeling in Pulmonary Arterial Hypertension
Authors: Bordan Zsuzsanna , Chen Feng , Li Xueyi , Batori Robert , Haigh Stephen , Meadows Mary-Louise , Singla Bupesh , Csanyi Gabor , Su Yunchao Karoly , Barman Scott Karoly , Fulton David 
Published: April 2020

Pulmonary Arterial Hypertension (PAH) is an insidious disease that develops gradually and becomes symptomatic only in the latter stages. In PAH, along with increased pulmonary artery (PA) pressure, the PAs in the lungs continue to become more muscular, narrower restricting blood flow through the lungs. Increased proliferation of pulmonary arterial smooth muscle cells (PASMC) are largely responsible for the development PA hypertrophy. Because excessive proliferation of PASMC in PAH shares many characteristics with other hyperproliferative diseases such as cancer, there is a growing interest in repurposing therapeutic targets in cancer, for the treatment of PAH. In preliminary studies, we screened a microarray of isolated PAs from control and monocrotaline (MCT)‐induced PAH rats for novel genes that may be responsible for the proliferation of PASMCs in PAH. We found that the gene PDZ‐Binding Kinase (PBK) was significantly higher in PAs from MCT rats versus controls. PBK (also known as TOPK or T‐cell‐originated Lymphokine‐activated killer protein kinase) is a serine/threonine kinase that plays a key role in several types of cancer. Although PBK levels are typically very low in healthy tissues, expression levels are significantly increased in cancer cells, which correlates with a poor prognosis of breast, gastric and lung cancers. We performed immunostaining, and found that PBK was highly upregulated and concentrated in the smooth muscle layer of both PAH rats (MCT and Sugen/Hypoxia induced) as well as in human PAs with PAH. To determine a functional role for PBK in PASMCs, we generated an adenovirus encoding PBK and found that increased expression stimulated PASMC proliferation and resistance to apoptosis. In contrast, silencing PBK or in vitro pharmacological inhibition (HI‐TOPK‐032, 2μM) significantly (p<0.05; n=5) reduced PASMC proliferation and increased cell death. Furthermore, the specific PBK inhibitor OTS514 (5mg/kg/day for 14 days) reduced right ventricle hypertrophy (Fulton Index) and improved PA remodeling in the MCT‐induced model of PAH. Collectively, these findings suggest that PBK drives pulmonary artery smooth muscle proliferation leading to abnormal vascular remodeling and the development of PAH.Support or Funding InformationAHA 19PRE34450087R01HL125926‐03
Importance of Selected Acinetobacter AAC(6′)‐Ig Active Site Residues on Escherichia coli Susceptibility to Aminoglycosides
Authors: Barol Irina , Pradhananga Anjani , Pennings Pleuni , Kuhn Misty L. 
Published: April 2020

Aminoglycosides are broad‐spectrum antibiotics commonly used to treat infections caused by Gram‐negative pathogens. However, bacteria become resistant to these antibiotics by acquiring or utilizing innate aminoglycoside acetyltransferases (AACs) that modify the drug. For instance, Acinetobacter haemolyticus has acquired the AAC(6′)‐Ig enzyme and is resistant to multiple aminoglycosides. However, our current understanding of the key residues of the active site that are critical for enzymatic activity of this enzyme is limited. Therefore, we selected two residues in the active site of the protein that formed either H‐bonds or exhibited pi‐pi stacking with tobramycin in the 3D structure of the enzyme and mutated them to bulky or charged amino acids. Next, we examined the susceptibility of Escherichia coli in the presence and absence of these over‐expressed Acinetobacter proteins toward four aminoglycosides. We found the identity of the residue substituted at these positions altered their susceptibility to these antibiotics, which provides insight into how this enzyme recognizes and modifies its diverse substrates.Support or Funding InformationResearch reported in this work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM133506 (to MLK).
Foot compartments. How many and it’s clinical relevance
Authors: Quiroga-Garza Alejandro , Vázquez-Zorrilla Daniel , Millan-Alanis Juan Manuel , Alvarez-Villalobos Neri Alejandro , Salinas-Alvarez Yolanda , Guzman-Lopez Santos , Elizondo-Omaña Rodrigo Enrique , Fernandez-Rodarte Bernardo Alfonso 
Published: April 2020

IntroductionSeveral authors have assessed the foot with diverse methods, with discrepancies towards the number of compartments. Treatment for foot compartment syndrome is not standardized, but primarily consists of liberating pressure from these, to avoid ischemia, nerve damage, and malformation. Our objective is to synthesize the existing evidence regarding the compartmental anatomy of the footMaterials and methodsA systematic review of all publications evaluating normal foot compartment anatomy was performed using the MEDLINE, Scopus, Web of Science, and EMBASE databases. Data were recorded and analyzed by the reviewers.ResultsAfter filtering results, 10 studies were included in the final analysis. All were performed in cadavers except one. The primary difference was the region studied, half focusing on the plantar region, and the other half evaluating the whole foot. There seems to be an agreement regarding the number of compartments in the plantar region (three major compartments divided by the medial and lateral intermuscular septum), nevertheless, disagreements across authors tend to arise when describing its dorsal section. Only two studies were ranked with an overall low risk of bias using the AQUA checklist. These two agreed on 9 total compartments, however, one included the skin as a 10th compartment, although by definition (space occupied by tissue and bound by fascia or bone) it is not a compartment.ConclusionDiscrepancies in the number of compartments exist between authors. This review provides the best available evidence with an anatomical analysis of data and concludes 9 compartments of the foot. This anatomical description should be taken into account and referenced in clinical reports of foot compartment syndrome treatment to determine the best treatment in a future meta‐analysis based on the same classification.
GlyGen ‐ Computational Resources for Glycoscience
Authors: Tiemeyer Michael , Ranzinger Rene , Kashay Robel , Edwards Nathan , Mazumder Raja , York William 
Published: April 2020

Advancing our understanding of the roles that glycosylation plays in development and disease is frequently hindered by the diversity of the data that must be integrated to gain insight into these complex phenomena. GlyGen is a maturing initiative, supported by the NIH Common Fund, with the goal of democratizing glycoscience research by developing and implementing a comprehensive data repository that integrates diverse types of data, including glycan structures, glycan biosynthesis enzymes, glycoproteins, three‐dimensional glycoprotein structures, along with genomic and proteomic knowledge. To achieve the highest possible integration and impact, GlyGen has established international collaborations with database providers from different domains (including but not limited to EBI, NCBI, PDB, GlyTouCan and UniCarbKB) and glycoscience researchers. Information from these resources and groups are standardized and cross‐linked to allow queries across multiple domains. To facilitate easy access to this information, an intuitive, web based interface (
http://glygen.org/) has been developed to visually represent the data and the connections between datasets. In addition to the browser‐based interface we are also developing RESTful webservice‐based APIs and SPARQL endpoints, allowing programmatic access to integrated datasets. For each glycan and glycoprotein in the dataset, GlyGen provides a details page that integrates available information. Individual details pages are interlinked with each other allowing easy data exploration across multiple domains. For example, users can browse from the webpage of a glycosylated protein to the glycan structures that have been described to be attached to this protein, and, from there, to other proteins that carry the same glycan. All information accessed through GlyGen is linked back to original sources, allowing users to browse through information pages in other resources. Our goal is to provide scientists with an easy way to access the complex information underlying state‐of‐the‐art knowledge that describes the biology of glycans and glycoproteins. To maximize usefulness of the GlyGen resource by the broadest possible user population, we have implemented a query interface that suggests likely “use‐case” questions. For instance, a question such as “What are the enzymes involved in the biosynthesis of glycan X in humans?” can be posed simply by providing minimal information (e.g. glycan X in the example). Answers are then returned following the completion of a query across multiple datasets and domains; the complexity of the query remains invisible to the user. Importantly, use‐case questions were developed as a result of outreach to potential users through community meetings and directed contacts. To schedule a demo of GlyGen or add your data to GlyGen contact Michael Tiemeyer (
mtiemeyer@ccrc.uga.edu) or Raja Mazumder (
mazumder@gwu.edu).Support or Funding InformationSupported by NIH Common Fund U01 GM124267‐01
Calcium‐Dependent Dual Oxidase 2 is a Novel Source of Reactive Oxygen Species Implicated in Glomerular Mesangial Cell Fibrotic Response to Angiotensin II
Authors: Baistra Teresa , Tristan Anais , Ford Bridget Marie 
Published: April 2020

The vasoactive peptide angiotensin II (Ang II) contributes to the initiation and the progression of glomerular fibrosis via activation of glomerular mesangial cells (MCs) and subsequent extracellular matrix expansion. We have previously shown that oxidative stress is critical for MC fibrotic response to Ang II. Here, we demonstrate that Dual oxidase 2 (Duox2), a member of the Nox/Duox family of NADPH oxidases, is present in MCs and that its protein expression is upregulated by Ang II.Small interfering RNA (siRNA)‐mediated downregulation of Duox2 significantly reduces Ang II‐induced increase in reactive oxygen (ROS) generation and prevents the stimulatory effect of Ang II on MC fibrotic injury (as assessed by measuring α‐smooth muscle actin and fibronectin expression).To demonstrate that Duox2 activation is Ca2+‐dependent, we show that the extracellular Ca2+ chelator BAPTA prevented Ang II‐induced ROS generation and the stimulation of MC fibrotic injury by Ang II. Moreover, treatment of MCs with ionomycin resulted in increased ROS production and enhanced MC fibrotic injury. These effects were abrogated by siRNA targeting Duox2. Fura‐2 fluorescence was utilized as well to show calcium mobilization in response to Ang II and this effect was abrogated with siDuox2 transfection. These data indicate that Ang II‐stimulated Duox2 activation and ROS generation subsequently lead to MC fibrotic injury.In summary, we have identified a novel role for Duox2 as a major source of ROS in response to Ang II and established the significance of Duox2 in Ang II‐mediated MC activation and fibrotic injury. Therapeutic targeting of this pathway may prevent or reverse pathophysiologic manifestations of renal fibrotic diseases.Support or Funding InformationThis project was funded by the University of the Incarnate Word, Office of Research and Graduate Studies and the following grants: NRSA 5T32HL007446‐32