bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary Toxicity of Nine Sand Dusts Generated at Hydraulic Fracturing Sites in Comparison to Respirable Crystalline Silica
Authors: Fedan Jeffrey S. , Barger Mark , Leonard Stephen S. , Thompson Janet A. , Snawder John E. , Dozier Alan , Coyle Jayme , Kashon Michael , Roberts Jenny R. 
Published: April 2020

The levels of respirable crystalline silica (RCS) at gas wells employing hydraulic fracturing (fracking) sites have been reported to exceed regulatory standards. Inhalation of RCS in work places may cause silicosis and other diseases in workers. While the effects of inhalation of RCS in humans and animal models has been well‐characterized, the pulmonary hazards to worker associated with RCS inhaled at fracking sites has not been investigated. In this study, nine fracking sand dusts(FSDs) collected by vacuum dust controls from different fracking sites in the US were compared to MIN‐U‐SIL 5® (MIN) with respect to particle size, mineral composition, Si radicals and pulmonary toxicity. Chemical analysis revealed that total mineral content of the FSDs other than Si ranged widely from 9.9 g/kg to 32.5 g/kg when compared to 1.4 g/kg for MIN. This heterogeneity was confirmed by energy‐dispersive X‐ray spectroscopy (EDS). Hydrodynamic particle diameter of neat FSDs using dynamic light scattering (DLS) indicated non‐concordant, mono‐ orbi‐modal spectral distributions of particle sizes; the spectrum for MIN was mono‐modal. Electron paramagnetic resonance (EPR) analysis indicated the presence of the Si radical in MIN but not in neat FSDs. After incubating the FSDs in water the Si radical was revealed in some samples, indicating occlusion of the radical in neat FSDs. To examine pulmonary toxicity, rats were intratracheally instilled with a single dose of FSD or MIN (159 or 500 μg/rat), or vehicle. Thirty days later, bronchoalveolar lavage (BAL) was performed to assess the development of pulmonary inflammatory responses: changes in lactate dehydrogenase (LDH) and differential cell counts. This time point has been shown previously to be one at which pre‐silicotic responses to MIN are observed. As expected, MIN elicited a dose‐dependent increase in LDH levels, total BAL cells, and total alveolar macrophages, polymorphonuclear lymphocytes and eosinophils. As a group, the FSDs did not elicit these responses. These findings indicate that, in many respects, the chemical and biophysical characteristics, and the biological effects of the FSDs and MIN after intratracheal instillation, have distinct differences.Support or Funding InformationNIOSH 6927ZLDC
Role of Na+/H+ Exchanger 1 in Regulating Resistance to Apoptosis in Pulmonary Arterial Smooth Muscle Cells
Authors: Munson Micheal , Yun Xin , Jiang Haiyang , Philip Nicolas , Huetsch John , Shimoda Larissa 
Published: April 2020

Vascular remodeling within the pulmonary arterioles is a key component of pulmonary arterial hypertension (PAH). In a rat model of severe PAH, the SU5416‐Hypoxia (SuHx) model, pulmonary arterial smooth muscle cells (PASMCs) demonstrate resistance to apoptosis and contribute to vascular remodeling. Na+/H+ exchange (NHE) is increased in SuHx PASMCs; however, few studies have elucidated the functional role of NHE in these cells. Previous studies have shown a link between NHE and the expression of CHOP, a critical mediator of apoptosis. Therefore, we tested the hypothesis that altering NHE1 expression and or activity is sufficient to modulate apoptosis in PASMCs. PASMCs were isolated from distal pulmonary arteries dissected from vehicle‐treated, male, Wistar rats or rats exposed to hypoxia after an injection of SU5416 (SuHx rats). PASMCs were treated with vehicle, a combination of a pharmacologic inhibitor of NHE (EIPA) and hydrogen peroxide (H2O2), an apoptosis‐inducing agent, or either EIPA or H2O2 alone. Apoptosis was measured via Hoechst staining. In other experiments, control PASMCs were infected with a viral construct to overexpress wild‐type NHE1 (AdNHE1), a translocation‐disabled NHE1 mutant (AdE266I), or green fluorescent protein (AdGFP) as a control. NHE activity was measured via the ammonium‐pulse technique. SuHx PASMCs exhibited decreased CHOP expression and minimal apoptosis rates in response to H2O2 when compared to control PASMCs. EIPA had no effect on unstimulated apoptosis in control cells, but induced apoptosis in SuHx PASMCs at baseline and sensitized the cells to H2O2. AdNHE1, but not AdE266I, increased NHE1 activity. Interestingly, both AdNHE1 and AdE266I conferred a resistance to H2O2‐induced apoptosis when compared to the AdGFP‐infected cells. Overall, these findings suggest that increased NHE1 may be responsible for attenuating apoptotic responses in SuHx PASMCs and that increasing NHE1 levels in normal PASMCs is sufficient to promote increased survival via an ion‐translocation‐independent function.Support or Funding InformationSupported by NIH grants HL073859, HL126514 and HL084762
Role of Mucin‐1 in Carcinomas
Authors: Link Tina , Caruso Olivia , Kona Abhishek , Lu Allison , Saberi Zara , Shabazaz Tara , Vijay Varun 
Published: April 2020

Mucin 1 (MUC1) is a large, heavy O‐glycosylated mucin glycoprotein with a molecular weight of 250 to 500 kDa, depending on the level of glycosylation, and extends 200–500 nm from the cell surface. MUC1 spans the cell membrane at the apical surface of normal simple epithelia and the surfaces of some hematopoietic cells. MUC1 is comprised of three major domains: the cytoplasmic tail, transmembrane, and extracellular domains. The cytoplasmic tail (CT) domain is highly conserved across species and interacts with various cell signaling networks. The transmembrane domain is composed of hydrophobic amino acids to anchor MUC1 in the membrane. The extracellular domain is not strictly conserved, but always consists of a series of 20–100 tandem repeats enriched in serine, threonine and proline residues providing sites for the heavy O‐linked glycosylation characteristic of mucin‐type glycoproteins. The extracellular domain contributes MUC1’s function as an inhibitor of cell‐cell and cell‐extracellular matrix adhesion. The heavy glycosylation of MUC1 normally serves to protect cells from infection and also lubricates the cell surface. In normal biology, MUC1 serves as an inhibitor of embryo attachment to the uterine cell surface and controls early aspects of the reproductive process. In cancer, carcinomas often overexpress MUC1 due to a combination of gene duplication events as well as stimulation of MUC gene expression by cytokines produced by cells of the immune system in their efforts to destroy the cancer cells. Cancer cells also lose their normally polarized distribution of MUC1 and instead express the glycoprotein over their entire surface, MUC1 protects tumor cells from the immune system in two ways. First, by inhibiting the cell contact required for cell‐mediated immunity, e.g. by NK cells. In addition MUC1 expressed at tumor cell surfaces or shed by the action of cell surface proteases is immunosuppressive, presumably by interacting with immune checkpoint inhibitors. Various mouse models have been used to conduct research about MUC1, showing the connection between MUC1 overexpression in mouse mammary glands and cancer development and other processes. MUC1 serves as a commonly used serum marker for various cancers and is being explored as a target for certain therapeutic approaches. The Walton SMART team has designed a 3D model of MUC1 to investigate the relationship between its structure and function.Support or Funding InformationMSOE Center for Biomolecular Modeling
Concomitant NFE2L2 and CTNNB1 mutations in a subset of HCC patients: Synergy between Nrf2 and Wnt pathway in hepatocarcinogenesis
Authors: Tao Junyan , Liu Silvia , Bell Aaron , Monga Satdarshan P 
Published: April 2020

BackgroundHepatocellular cancer (HCC) remains a major clinical need with gradually increasing incidence and currently lacks precision therapy. Thus, there is a need to better characterize molecular drivers in HCC and generate relevant models to test biology and therapies. In the USA, CTNNB1 mutations occur in 26% of all HCCs, however they alone are insufficient to lead to tumors as shown by preclinical studies suggesting cooperation with other pathways.MethodsWe assessed TCGA and other publically available databases for aberrations that co‐occur with CTNNB1 in HCC cases. We used sleeping beauty transposon/transposase (SBT) to express such clinically relevant mutants in a subset of hepatocytes in vivo in mice using hydrodynamic tail vein injection (HTVI). Specifically, we co‐delivered T41A‐CTNNB1 and wild type (WT)‐NFE2L2, G31A‐NFE2L2 or T80K‐NFE2L2 into 6–8 weeks old FVB mice via SBT‐HTVI and assessed tumorigenesis over time. WGS was performed on mouse tumors to identify differentially expressed genes and pathways. Similarity between the mouse model and human HCC subset was addressed by overlap between the most significantly altered pathways.ResultsOf the 377 HCC patients in TCGA, 99 patients showed CTNNB1 mutations. Analysis for Nrf2 pathway showed 15 HCCs with NFE2L2 and 18 with KEAP1 mutations. 12 patients showed coexistence of CTNNB1 mutations with wither NFE2L2 (n=6) or KEAP1 (n=6). Co‐expression of T41A‐CTNNB1 with G31A‐NFE2L2 or T80K‐NFE2L2 but not WT‐NFE2L2 led to HCC by 13–14 weeks. H&E staining confirmed the presence of well‐differentiated HCC. Immunostaining and WB showed HCCs to be strongly positive for b‐catenin targets (GS and pmTOR) and also for Nrf2 targets including NAD(P)H dehydrogenase [quinone] 1 and peroxiredoxin‐1. Next RNA‐Seq analysis on tumor‐bearing livers in mice using FDR=0.1 as cutoff showed many significantly altered pathways. Analysis of Nrf2‐CTNNB1 mutant HCC in TCGA also identified 64 pathways that were significantly altered using the FDR=0.1 as cutoff. 21 common and significant pathways were identified between our mouse model and patients, which have well known correlation with HCC development.ConclusionsThus, Nrf2 and Wnt pathway cooperate in HCC pathogenesis in a subset of patients. Co‐expression of mutant NFE2L2 and mutant CTNNB1 leads to HCC in mice with notable similarity in pathway alterations to the human HCC subset. This will be a valuable model to study biology and treatment for this subset of HCC cases.Support or Funding InformationThis work was supported by NIH grants R01CA204586 to S.P.M
The sigma‐1 agonist PRE‐084 protects against energy depletion induced barrier disruption and also enhances glycolysis in HUVECs
Authors: Motawe Zeinab Y. , Farsaei Forouzandeh , Abdelmaboud Salma S. , Cuevas Javier , Breslin Jerome W. 
Published: April 2020

The sigma‐1 receptor (σ1) is a well‐known endoplasmic reticulum (ER) chaperone that resides at the mitochondria‐associated ER membrane, having an important role in calcium signaling between ER and mitochondria. Expression of σ1 is present in all human tissues with specific predominance in arteries, liver, fibroblasts and brain. Our laboratory has shown that σ1 activation in lymphatic vessels elicits nitric oxide‐dependent lymphatic relaxation, a finding that suggested the potential important role of σ1 in endothelium. Other recent work has highlighted that σ1 may contribute to healthy endothelial barrier function, although little is known about the mechanisms involved. We hypothesized that σ1 helps protect the endothelial barrier disruption by stabilizing cellular bioenergetics. Cultured human umbilical vein endothelial cell (HUVEC) monolayers were used to model the endothelial barrier. Electric cell‐substrate impedance sensing (ECIS) was used to study the contribution of σ1 to endothelial barrier function. Western blotting was used to quantify σ1 protein expression. Endothelial bioenergetics were determined with extracellular flux analysis using glycolytic rate and ATP rate assays. The endothelial‐specific contribution of σ1 was assessed using with the σ1‐selective agonist PRE‐084 and by specific siRNA knockdown of σ1. The mitochondrial un‐coupler Carbonyl cyanide m‐chlorophenyl hydrazine (CCCP) was used to model mitochondrial dysfunction in HUVEC. Our results show that activation of σ1 with PRE‐084 50 μM, 100 μM, 150 μM, 200 μM significantly enhances barrier function of HUVEC monolayers in a concentration‐dependent manner. Knockdown of σ1 with siRNA reduces baseline barrier function and diminishes the ability of PRE‐084 to enhance TER. The decrease in TER elicited by CCCP (10 μM) is significantly amplified in cells with siRNA‐mediated knockdown of σ1 expression, and is reversed by PRE‐084 (100 μM) in cells with normal σ1 expression. HUVEC treated with PRE‐084 display higher levels of glycolysis and glycolytic ATP production than control cells. This response to PRE‐084 was not evident in the presence of σ1 knockdown. Collectively, our results suggest that σ1 plays an important role in maintenance of baseline endothelial barrier function, and that activation of σ1 can enhance barrier function. Moreover, σ1 activation also can rescue endothelial barrier dysfunction caused by disruption of mitochondrial ATP production, likely due to its ability enhance glycolysis. Thus, σ1 may represent a future therapeutic target to rescue endothelial barrier dysfunction.Support or Funding InformationThis work was supported by NIH Grant R01GM120774.
Selective optogenetic stimulation of RTN neurons drives ventilation and active expiration in unanesthetized rats
Authors: Souza George M. , Stornetta Ruth L. , Stornetta Daniel S. , Abbott Stephen B.G. , Guyenet Patrice G. 
Published: April 2020

BackgroundThe retrotrapezoid nucleus (RTN) consists of neurons that are chemosensitive (i.e., CO2/pH sensitive), glutamatergic, Phox2b+ and Neuromedin B+ (Nmb+). Lentiviral vectors currently used to transduce RTN neurons with various opto‐ or pharmacogenetic actuators contain a Phox2b‐activated promoter, PRSx8. When injected into the RTN, these vectors also transduce substantial numbers of nearby C1 and catecholaminergic neurons. The purpose of the present study was to determine the effects on breathing elicited by selectively activating RTN neurons.MethodsTo selectively transduce RTN neurons we microinjected a mixture of Lenti‐PRSx8‐ChR2‐mCherry and AAV5‐FLEX‐taCasP3‐TEVp into the RTN of adult TH‐Cre rats. One month after the surgery, RTN neurons were stimulated with blue light (473 nm, 10 ms pulse, 20 Hz, for 20 s). All the measurements were conducted inside a plethysmography chamber. Diaphragm (DIA) and abdominal (ABD) muscle activity were recorded in conscious conditions. Results (mean ± SD), were analyzed using one‐ or two‐way ANOVA as required and differences were considered significant at P<0.05.ResultsRTN neurons (Nmb+, TH−) were selectively transduced (96.8 % ± 4) with the PRSx8 vector, the FLEX‐caspase AAV5 having caused the apoptotic death of C1 neurons (TH+) in the area where neurons were transduced with ChR2. Selective stimulation of RTN (NMB+ neurons; n=6) increased respiratory rate during wake and NREM sleep but not during REM sleep (Δ 30 ± 7 vs. 22.7 ± 6 vs. 4 ± 4 bpm from baseline), increased tidal volume also during quiet waking and non‐REM but not REM sleep (Δ 0.15 ± 0.07 vs. 0.13 ± 0.04 vs. 0.02 ± 0.007 mL/100g) and VE also during wake and non‐REM sleep but not REM (27.8 ± 11 vs. 21.4 ± 8 vs. 3.1 ±1 mL/100g/min). Selective RTN stimulation in rats breathing room air elicited active expiration (from 8.4 ± 7 to 15.9 ± 8 % of normalized abdominal EMG recorded at 9% FiCO2, n=3). RTN stimulation produced greater active expiration in rats exposed to 6% FiCO2 (from 56.3 ± 32 to 125.3 ± 104 % of normalized abdominal EMG).ConclusionsSelective RTN neuron stimulation drives breathing amplitude and frequency during wake, NREM but not in REM sleep, and elicits active expiration, especially at elevated levels of FiCO2.Support or Funding InformationSupported by grants from the National Institutes of Health (HL28785, 18 HL074011) and the Congenital Central Hypoventilation Syndrome Foundation to PGG.
Ontogenetic Trends in Frontal Sinus Shape
Authors: Butaric Lauren , Garvin Heather , Zimmerman Kristine 
Published: April 2020

Adult frontal sinus morphology has been studied in biological anthropology, both in terms of its function and variation. Overall, this structure is known to be highly variable among individuals, to such an extent that it is used to make positive identifications in the medicolegal setting. However, very little is known about the growth and developmental processes leading to the wide ranges of frontal sinus size and shape. Although several studies investigate frontal sinus ontogeny in terms of size and linear dimensions, much less is known regarding the ontogeny of its shape. This study partially addresses this gap by examining frontal sinus outlines using longitudinal radiographic data to evaluate when the frontal sinus attains its adult shape.Longitudinal radiographs for 107 individuals (57M/50F) spanning 5–29 years of age (yoa) were obtained from the AAOF Craniofacial Growth Legacy Collection (
www.aaoflegacycollection.org). Superior borders of frontal sinus outlines were digitally traced in ImageJ; the superior orbital border demarcated inferior sinus boundaries. Age of first appearance was also recorded. A total of 749 outlines were imported into SHAPE‐software, where elliptical Fourier (20 harmonics) and principal components (PC) analyses were conducted. PC1 (49.18% variation explained) reflects height‐to‐breadth relationships, while PC2 (11.74%) reflects asymmetry in right versus left lobe dominance.To assess when the frontal sinus attains its adult shape, Euclidean distances of PCs 1–9 (91.58% cumulative variance) between each age point and the 18‐year point were calculated within individuals; this process was repeated for the 20‐year point. Scatterplots with Loess curves for each distance plotted against age suggest adult shape is attained around 20yoa. Sexual dimorphic trends are evident in the Loess curves, whereby males exhibit greater distances from 20yoa at early ages. An analysis of variance confirms these sex‐based differences (F=7.063, P<0.0001); Tukey post‐hocs further suggest that while adult females are not significantly different in shape from adult males or younger females/males (13–19yoa), adult males are significantly different from males 15yoa and younger. T‐tests failed to find significant sex‐based differences for age‐of‐first‐appearance (t=1.482, P=0.142) and adult‐shape (PC1: t=−0.670, P=0.505; PC2: t=1.827, P=0.058). Thus, it appears that while both sexes display similar start times in sinus development and reach similar adult‐shapes, females attain their adult shape sooner. This suggests a slower developmental process in males. Additional studies are needed to determine how these ontogenetic patterns in 2D sinus‐shape relate to the overall size and 3D dimensions of the sinus.
Developing a 3D Physical Model of HIV Protease to Explore Drug Resistance to Tipranavir and Darunavir
Authors: Dyrma Sherina , Van Acker Cyndi , Nooh Asha , Palacios Alessia , Martinez-Vaz Betsy 
Published: April 2020

HIV infections affect over 38 million people worldwide and cause approximately one million deaths every year. Despite advances in antiretroviral therapies and disease prevention strategies, drug resistance remains a major challenge in HIV treatment. HIV protease plays a key role in viral replication by facilitating the peptide bond hydrolysis reactions necessary for the development of functional viral particles. Diverse inhibitors have been developed to target the active site and substrate envelope of HIV protease. While these drugs have been effective at inactivating the enzyme, mutations at the active site give rise to HIV resistance strains which are insensitive to protease inhibitors. The goal of this project was to create 3D printed models of HIV protease to illustrate the mechanisms of action of two inhibitors, Tipranavir and Darunavir, and the mutations involved in the development of resistance to these drugs. Database searches and sequence alignments were performed to identify conserved amino acids and structural features important in the catalytic mechanism of HIV proteases. Details of the protein structure and its interaction with Tipranavir and Darunavir were obtained by analyzing the Protein Databank Files: 6DIF, 6DGX, 6OPS, and 6DH6. To construct the physical models, the structure files were imported into Jmol and modified into a format suitable for 3D printing using scripts created by undergraduate researchers. The 3D models feature the overall structure of HIV protease, and its inhibitor molecules, Tipranavir and Darunavir. An active site box was constructed to illustrate the biochemical interactions between the enzyme and the inhibitors. The physical models also highlight key amino acids such as Asp25, Ile50, Val82, and Val84, which are critical for catalytic activity and the development of drug resistance. Magnetic pieces were created to show the effects of mutations in inhibitor binding and enzyme activity. A Jmol tutorial was designed to complement the 3D models and assess students’ learning of the structure and function of HIV protease.Support or Funding InformationThis project is funded in part by NSF‐IUSE #1725940 for the CREST Project.
Verification of aortic arch variations through modern imaging
Authors: Hirtler Lena , Tucheslau Moritz 
Published: April 2020

IntroductionThe aortic arch with its vessels offers one of the biggest varieties of branching patterns, which is barely beeing mentioned in modern medical textbooks though. The last big survey on the most common varieties had been published by Lippert in 1967 and, since then, not been verified, just republished. With these varieties being of great importance in certain fields of medicine, the up‐to‐dateness of Lippert’s data has been analysed.AimThe main objective is the analysis of CT‐Angiographies for branching varieties of the aortic arch and comparison of frequency distributions with Lippert 1967. The secondary objective is measuring the vessel lumen of varieties and comparison with matches of the standard variant to find out if varieties have influence on the vessel’s lumen.Material/MethodsThis retrospective cross‐sectional study includes 400 patients, more specificaly their CTAs from 01.01.2017 to 31.12.2017, obtained from the University Department of Biomedical Imaging and Image‐guided therapy, General Hospital Vienna. Incusion and exclusion criteria have been differently set up for main and secondary objective. Patients for the main objective have been excluded if they have had any kind of surgery altering their varieties, like bypass‐surgery. Patients for the secondary objective have have been excluded if they were under the age of 18 or have had any kind of diseases/surgery altering the supraaortic vessel’s lumen.The main objective has been represented with tabular comparisons. For the secondary objective patients not fulfilling the criteria have been excluded at first. Afterwards the different groups of varieties have been matched with groups of the standard variant similiar in age and distribution of sex. The vessel’s lumen then has been analysed and t‐tested.ResultsThe analysis and comparison of data in terms of frequency have been proved statistically in‐significant. Testing of V2_TBv with V1_TB (p<0,001; α=0,05) as well as V2_ACCS with V1_ACCS (p<0,001; α=0,05) have shown statistical significance.ConclusionDespite minor deviation after analysis with modern imaging the data of Lippert from 1967 can still be seen as up‐to‐date. In vascular surgery it may be neccessary to be considerate about the vessel lumen in case of any known variety of the branches of the aortic arch. Certain questions may ask for more detailed analysis.