bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Reactive Neurogenesis in the Forebrain of the Leopard Gecko (Eublepharis macularius)
Authors: Austin Laura E. , Graham Chloe A. , Vickaryous Matthew K. 
Published: April 2020

Neurogenesis is the ability to generate new neurons from resident progenitor populations. Although best understood as a normal physiological process, in several species of teleost fish and salamanders neurogenesis is also capable of replacing neurons lost or damaged due to injury – so called reactive neurogenesis. While reactive neurogenesis does not appear to resolve brain injuries in mammals, for reptiles less is known. Here, we investigated reactive neurogenesis in the lizard Eublepharis macularius, the leopard gecko. To initiate reactive neurogenesis, we administered geckos with a single dose of the neurotoxin 3‐acetylpyridine (3AP). Using the cell death markers Fluoro‐Jade and the TUNEL assay, we determined that neuronal loss occurs within 4 days following 3AP administration. Cell death is largely restricted to the medial and dorsomedial cortices, areas of the forebrain widely accepted to be the reptilian homologs of the mammalian hippocampus and neocortex, respectively. As evidenced by a decrease in the number of cells expressing the mature neuronal marker NeuN, cell death within these regions appears to selectively target neurons. Remarkably, by 30 days following 3AP administration the medial and dorsomedial cortices appear to be structurally restored with a pattern of NeuN expression that closely resembles the uninjured brain. These data provide the first evidence that the leopard gecko is capable of reactive neurogenesis, a phenomenon otherwise rare among amniotes (reptiles and mammals).Support or Funding InformationNatural Sciences and Engineering Research Council (NSERC), Discovery Grant 400358)
Characterization of the Transcription Termination Factor Responsible for Polarity in Archaea
Authors: Wu Wenrun 
Published: April 2020

The absence of a nuclear compartment permits prokaryotic ribosomes to bind nascent RNAs to initiate translation before a transcript is completely synthesized. Transcription and translation are normally tightly coupled in prokaryotes (Archaea and Bacteria) and uncoupling translation from transcription serves as a regulatory signal, permitting premature transcription termination when translation fails or is inhibited. The resultant decrease in downstream gene expression, termed polarity, is a major regulatory pathway to ensure coordinated gene expression. While the importance and widespread use of polar repression is well documented, to date, the factor responsible for polarity in archaea cells has not been explicitly identified.In bacteria, the transcription termination factor rho is responsible for polarity, but there are no rho homologues encoded in archaeal genomes. FttA (Factor that terminates transcription in Archaea), a recently identified archaeal termination factor, appears to potentially fulfill the requirements to direct polarity in archaea, but other factors may be responsible. Our primary objective, employing an unbiased genetic selection, is to identify the transcription termination factor(s) responsible for polar repression in Archaea.We have established and will present our findings resultant from a three‐tiered genetic selection for spontaneous mutations that impact the efficiency of polar repression in archaeal cells. The selections were carried out in specialized strains of Thermococcus kodakarensis, a marine, hyperthermophilic archaeon with a facile genetic system and robust laboratory growth.Briefly, genomic modifications were introduced to place a non‐essential gene with a premature translation stop codon directly upstream and within the same operon of a reporter or essential (selection) gene. In wide‐type strains, the early stop codon permits a polarity factor to recognize uncoupling of transcription and translation and terminate transcription before productive expression of the downstream essential gene. However, when the activity of a polarity factor(s) is hindered, these selective genes can be expressed at high levels. For selection, the final genes of the tryptophan and histidine synthesis pathway were chosen, constructing auxotrophic mutant strains which can only develop in the absence of tryptophan and histidine if there is some disruption in polarity‐ allowing them to become prototrophic. The spontaneous mutations resultant in reduced polar repression are easily identified through whole‐genome sequencing and we present evidence for roles of multiple factors in mediating polarity in archaeal cells.
SPARC: Deep Learning for Stomach Segmentation with Contrast Enhanced Magnetic Resonance Imaging of the Gastrointestinal Tract
Authors: Wang Xiaokai , Lu Kun-Han , Choi Minkyu , Cao Jiayue , Jaffey Deborah , Powley Terry , Liu Zhongming 
Published: April 2020

Contrast‐enhanced magnetic resonance imaging of the gastrointestinal tract (gMRI) enables non‐invasive assessment of gastric emptying and motility and provides imaging‐based evaluation of pharmacological or bioelectrical treatment of gastric disorders. For both purposes, robust image processing is required to segment the gastrointestinal tract, separate its compartments, capture its dynamics, and quantify its physiology or pathology. Due to the complex anatomy and dynamics of the gastrointestinal tract, conventional image processing methods are hard to generalize across animals or species, are semi‐automatic, time‐consuming and in need of manual correction.Here, we reported a deep learning algorithm to segment the gastrointestinal tract based on 3‐dimensional (3D) contrast‐enhanced gMRI. Specifically, we constructed a 3D U‐net with an encoder‐decoder architecture in which convolutional layers were connected in a U‐shape. The encoder took the gMRI images as its input and learned a representation of the input; the decoder used the learned representation to generate pixel‐wise classification for segmentation of the stomach and small intestines.To train and validate the U‐net, we used gMRI images (from 54 rats) segmented with a semi‐automatic processing pipeline as described in a prior paper. We used 1,047 3D volumes from 48 rats for training the model and used 139 volumes from 6 rats for validating the model. We found that the model was able to extract meaningful features to achieve accurate pixel‐wise classification on new image sets. The segmentation results were more accurate, consistent and generalizable than were previous algorithms. Quantitative evaluation suggested that the segmentation was highly accurate for the stomach (DICE=0.982±0.011) and reasonable for the small intestines (DICE=0.918±0.042). Importantly, this algorithm significantly reduced the processing time from >2 minutes to <1 second and thus was expected to be well suited for real‐time assessment.In conclusion, our model results in high segmentation accuracy and fast processing speed. It has the advantage over conventional methods and holds the unique promise to enable real‐time gMRI‐based assessment of gastrointestinal physiology. Future studies are desirable for using this technique to guide neuromodulation or pharmacological treatment of gastric disorders, e.g. gastroparesis.Support or Funding InformationNational Institutes of Health’s SPARC ‐ Stimulating Peripheral Activity to Relieve Conditions ‐ program (OT2OD023847)
Liver Diseases Contribute to Functional Platelet Aggregation Defects
Authors: Bacher Cassandra , Farooqui Ambar , Siddiqui Fakiha , Daravath Bharathi , Hoppensteadt Debra , Iqbal Omer , Fareed Jawed , George Magdalena , Van Thiel David 
Published: April 2020

IntroductionThe role of platelets in hemostasis involves their adherence to sites of vessel injury, aggregation to form plugs. Agents that physiologically activate platelets in vivo include adenosine diphosphate (ADP), epinephrine, collagen, thromboxane A2 (TxA2) and serotonin. Vascular and platelet dysfunction represent complications of hepatic disease. The purpose of this study is to investigate the effect of various agonists on platelet aggregation profile of patient with hepatic disease.Materials and MethodsIcteric Samples from the clinical lab from Loyola University medical center were randomly selected for this study (n=25). Blood samples from the healthy donors were included to prepare platelet rich plasma (PRP) and platelet poor plasma (PPP). PRP and PPP from various donors were separated to make pools. Four different pools were made namely Normal PRP, Icteric PRP, Icteric PRP + Normal PPP 1:1, Normal PRP + Icteric PPP1:1. Agonists such as ADP, arachidonic acid (AA), epinephrine and collagen were used to activate the platelets. The final assay concentration for ADP is 20 uM, AA is 500 ug/ml, collagen is 190 ug/ml and epinephrine is 10 ug/ml.ResultsAll results were compiled in terms of percent aggregation of platelets and represented as mean ± standard deviation. Normal PRP showed platelet aggregation response reaching a peak aggregation of 93.± 27.70 with ADP agonist. Icteric PRP, and two different pools did not show any significant platelet aggregation with ADP. Varying degrees of the inhibition of platelet aggregation was noted with epinephrine, collagen and arachidonic acid in comparison to normal PRP.DiscussionOn the basis of these results it is concluded that while the normal PRP showed platelet aggregation responses to various agonists’ icteric plasma, when mixed with normal PRP produced inhibition of platelet aggregation. This data suggests that the icteric plasma contains an endogenous substance which produces the inhibitory effect on agonist induced platelet aggregation.
Yeast Bax Inhibitor (Bxi1p/Ybh3p) is a calcium channel in E. coli.
Authors: Kalhorn John C. , Raffa Amanda P. , Strakosha Aleksander , Mullin James , Mello Nicholas , Austriaco Nicanor 
Published: April 2020

Human Bax Inhibitor‐1 (HsBI‐1/TMBIM6) is the founding member of the evolutionary conserved TMBIM superfamily of proteins that share sequence homology within the transmembrane Bax inhibitor‐containing motif (TMBIM). Mechanistically, BI‐1/TMBIM6 and all the other mammalian TMBIM proteins appear to be involved in the maintenance of calcium homeostasis, and the crystal structure of a bacterial TMBIM protein, BsYetJ, suggests that the protein is a pH‐sensitive calcium leak. The budding yeast, Saccharomyces cerevisiae, has a single TMBIM family member (YNL305C) named Bxi1p/Ybh3p. To determine the function of Bxi1p/Ybh3p, we overexpressed Bxi1p‐EGFP in E. coli to determine if it is a calcium channel. We show that bacterial cells expressing Bxi1p‐EGFP are more permeable to calcium than controls. Thus, our data suggests that yeast Bax inhibitor (Bxi1p) is a calcium channel in E. coli, lending support to our proposal that Bxi1p is a bona fide member of the TMBIM family of proteins. Further, we use our bacterial system to show that gadolinium is an inhibitor of Bxi1p in vivo, suggesting a path forward to identifying other small‐molecular inhibitors of this clinically‐important and highly conserved superfamily of proteins. Finally, parallel experiments revealed that the human Bax Inhibitor‐1 (HsBI‐1/TMBIM6) is also a calcium channel in bacteria that can be inhibited by gadolinium.Support or Funding InformationOur laboratory is supported by grant NIGMS R15 GM110578, awarded to N. Austriaco.
γ‐Tocotrienol Protects Against Mitochondrial Dysfunction, Energy Deficits, Tissue Damage, and Decreases in Renal Functions After Renal Ischemia.
Authors: Nowak Grazyna , Megyesi Judit , Che Yingni 
Published: April 2020

Renal ischemia is encountered in multiple clinical settings and frequently results in acute kidney injury (AKI) due to insufficient energy production to sustain renal functions. Ischemia‐induced mitochondrial dysfunction and ATP depletion result in disruption of the primary functions of the kidney in many affected hospitalized patients who suffer AKI, but are left without an effective treatment. This study tested whether γ‐tocotrienol (GT3), a member of the vitamin E family, promotes mitochondrial function, reduces ATP deficits and tissue damage, improves renal functions, and diminishes AKI after renal ischemia/reperfusion injury in mice. Mice were treated with vehicle or GT3 (200 mg/kg) 15h before or immediately after bilateral kidney ischemia, and end points were assessed in kidneys harvested at 24h, 72h, and 168h of reperfusion. GT3 treatment prior to and after ischemia reduced decreases in mitochondrial state 3 respiration and accelerated recovery of this function after ischemia. GT3 prevented the decreases in activities of NADH:Ubiquinone Oxidoreductase (complex I) and Ubiquinol:Cytochrome c Oxidoreductase (complex III) of the mitochondrial electron transport chain regardless of whether it was administered before or after ischemia. GT3 treatment also blocked ischemia‐induced decreases in ATP synthase (FOF1‐ATPase) activity and ATP content in renal cortical tissue. Furthermore, GT3 reduced renal tissue injury (decreased renal tubular necrosis and cast formation) and accelerated morphological regeneration of renal proximal tubules after ischemia. Kidneys of mice treated with GT3 displayed morphological improvements at 72h after ischemia by exhibiting fewer necrotic proximal tubules and inflammatory cells, while demonstrating increased tubular regeneration. GT3 treatment ameliorated increases in plasma creatinine levels and accelerated recovery of renal function after ischemia. Lastly, 89% of mice receiving GT3 and 70% of those receiving vehicle survived 72h after ischemia. In conclusions, GT3 administration improves mitochondrial respiratory functions and activity of FOF1‐ATPase, and prevents ATP deficits in ischemic kidneys. This is associated with improved kidney morphology, ameliorated decreases in renal functions, and increased survival after AKI.Support or Funding InformationThis research was supported by Arkansas Science & Technology Authority; Grant 15‐B‐27.
A novel integrated PK/PD model to assess combination therapy: Determination of the synergistic antitumor efficacy between doxorubicin and sorafenib
Authors: Choi Young-Hee , Zhang Chao , Liu Zhenzhen , Tu Mei-Juan , Yu Ai-Ming 
Published: April 2020

Understanding pharmacokinetic/pharmacodynamic (PK/PD) relationship is essential to identify optimal dosage regimens to achieve desired therapeutic outcomes. Existing PK/PD model for combination therapy lacks consideration of quantitative contributions from individual drugs while the “interaction factor” (y) may be arbitrarily assigned to one drug or the other. As such, distinct estimation and prediction results will be obtained, which will be confusing. In this study, we developed a novel integrated PK/PD model to characterize and predict combination therapy by considering contributions (e.g., a and β) from individual drugs (A and B, respectively), and established a new formula to define the “combination factor” (δ) concerning synergistic, additive, or antagonist effects. Doxorubicin (Dox; drug A) and sorafenib (Sor; drug B) were used as model drugs to validate this new approach. Dox (i.v.) and Sor (p.o.) PK data were obtained in BALB/c mice, and both were fit well to two‐compartment PK models. Physiological xenograft tumor growth was described by Simeoni model, and inhibition of tumor growth was attributable to the exposure to single drug (k2A×CA(t) or k2B×CB(t)), or combination (a×k2A×CA(t) + β×k2B×CB(t)). This PK/PD model was able to describe all experimental data, and reveal a greater antitumor potency for Dox (k2A = 13.8 L/mg/day) than Sor (k2B = 0.0267 L/mg/day), as well as a clear synergism (d = 1.24) for Dox plus Sor combination therapy with current dosage regimen. Interestingly, model simulation showed that increase of Sor doses for combination therapy preferably produces greater degrees of tumor suppression. Moreover, combination therapy with 2‐fold higher of tested Sor dose and half of Dox dose may lead to optimal synergistic antitumor effect. These results indicate that this new PK/PD model can be utilized to evaluate combination therapy in a definite manner.Support or Funding InformationThis study was supported by grants R01CA225958 and R01GM133888 from the National Institutes of Health
Depot‐Specific Response of White Adipose Tissue to MicroRNA‐21 Ablation in Polycystic Ovary Syndrome
Authors: Rezq Samar , Huffman Alexandra M. , Syed Maryam , Tiwari Suman , Basnet Jelina , Yanes Cardozo Licy L. , Romero Damian G. 
Published: April 2020

Background and aimPolycystic ovary syndrome (PCOS) is associated with obesity and insulin resistance. However, the molecular mechanisms that mediate this phenotype remain elusive. MicroRNA‐21 (miR‐21) is upregulated in PCOS and may be involved in the pathogenesis of the disease. We aim to study the role of miR‐21 in the deleterious metabolic effects associated with PCOS.MethodsThree week‐old miR‐21 knockout (miR21KO) or wild type (WT) female mice were treated with DHT (8 mg/silastic tube) or vehicle for 90 days (n=12/grp). Body composition was measured by EchoMRI. Energy expenditure (EE), oxygen consumption (VO2), and carbon dioxide production (VCO2) were measured by indirect calorimetry. Glucose homeostasis was measured by oral glucose tolerance test (OGTT). Gene expression was quantified by RT‐qPCR in subcutaneous (SC), retroperitoneal (RP) and mesenteric (M) white adipose tissue (WAT). Adipocyte size was evaluated by histological analysis.ResultsDHT increased body weight (25.07 ± 0.52 vs 21.79 ± 0.47 g, p<0.05), fat mass (4.60 ± 0.46 vs 1.98 ± 0.12 g, p<0.05) and adipocyte size (944 ±12 vs 513 ± 2 μm2, p<0.05), impaired OGTT (29.70 ± 2.21 vs 22.33 ± 1.06 AUC, p<0.05), and didn’t significantly change EE, VO2 or VCO2. Insulin signaling markers Irs1 and Slc2a4 expression was downregulated by DHT in all 3 WATs while Akt2 expression was upregulated. Adipogenesis markers Pparg and Adipoq were upregulated by DHT exclusively in the SC WAT. Inflammation marker Ccl2 was upregulated in all three WATs while Ikbkb was only upregulated in M WAT. Extracellular matrix (ECM) remodeling makers Mmp9 and Timp1 were upregulated by DHT only in RP and M WATs. Immune cells infiltration markers CD14, CD68, Itgam, Itgax, and CD86 were upregulated by DHT only in RP and M WATs.DHT‐treated miR21KO mice showed attenuated increase in body weight (23.84 ± 0.99 vs 25.07 ± 0.52 g, p<0.05) with no change in fat mass or OGTT. Additionally, DHT‐treated miR21KO mice showed a trend to reduced EE, VO2 and VCO2 compared with DHT‐treated WT. Gene expression data showed lower expression of the insulin signaling marker Akt2, higher expression of ECM remodeling markers (Mmp9 and Timp1) and an exacerbated inflammatory and immune responses in M (Il‐18 and CD14) and SC (Il‐18 and CD86) WATs. Moreover, DHT‐treated miR21KO mice had exacerbated adipocyte hypertrophy compared with DHT‐treated WT controls (1,408 ± 16 vs 944 ±12 μm2, p<0.05).Conclusion and significanceThese findings suggest that adipose tissue miR‐21 may have a protective role in PCOS and ameliorate some of the DHT‐mediated molecular changes observed in WAT in a fat depot‐specific manner. WAT‐specific modulation of miR‐21 levels could be a novel therapeutic approach for PCOS treatment.Support or Funding InformationSupported by National Institutes of Health grants P20 GM‐121334 (DGR and LLYC) and R21 DK‐113500 (DGR).
ERK3 Interacts with DGKζ and Alters Signaling Lipids in Lung Cancer Cells
Authors: Myers Amanda , Bedi Shimpi , Popp Katherine , Aldharee Hitham , Long Weiwen 
Published: April 2020

Extracellular‐Regulated Kinase 3 (ERK3) promotes migration and invasion in many cancers, including lung cancer. However, the mechanisms by which this atypical Mitogen‐Activated Protein Kinase (MAPK) induces these effects remain poorly understood. The p21‐activated kinase (PAK)‐Rac1 complex, which can be activated by phosphatidic acid, is associated with cell migration and has been shown to activate ERK3. Here, we show ERK3 also binds to phosphatidic acid and treatment of cells with phosphatidic acid results in an increase in ERK3 phosphorylation. Intriguingly, we have also found ERK3 modulates Rac1 activity and PAK phosphorylation, suggesting a positive feedback loop. In ERK3 knockdown cells, total diacylglycerol level was elevated while total phosphatidic acid level was decreased. In a yeast two‐hybrid assay, ERK3 was shown to interact with Diacylglycerol Kinase ζ (DGKζ), an enzyme which converts diacylglycerol to phosphatidic acid. This interaction has been confirmed by co‐immunoprecipitation and appears to occur through the C34 domain of ERK3. By immunofluorescence, these proteins were shown to co‐localize in cells with ERK3 enhancing cytoplasmic localization of DGKζ. Together, these data suggest ERK3 may regulate DGKζ to facilitate phosphatidic acid production, thereby activating the Rac1‐PAK complex and inducing cell migration.Support or Funding InformationNCI 1R01 CA193264‐01Wright State University start‐up fund
Pharmacopeia Potency Equated Sulodexide Produces Comparable Anticoagulation as Studied in Whole Blood
Authors: Daravath Bharathi , Bontekoe Emily , Kouta Ahmed , Iqbal Omer , Lattimer Christopher , Fareed Jawed 
Published: April 2020

IntroductionSulodexide is a widely used glycosaminoglycan derived drug for oral (antithrombotic) and parenteral (anticoagulant) indications and is composed of fast moving heparin (80%) and dermatan sulfate (20%). In view of the current shortage of porcine heparin supply sulodexide may be a potential substitute for heparin for surgical and interventional anticoagulation. The purpose of this study is to compare the anticoagulant activities of sulodexide with heparin in simulated studies to mimic surgical and interventional anticoagulation.Materials and MethodsPowder versions of sulodexide were obtained from Alfasigma (Bologna, Italy). Powder versions of porcine mucosal heparin were obtained from Medefil (Glendale Heights, IL, USA). Stock solution of both heparin and sulodexide were prepared in sterile saline at 10mg/ml. Sterile solutions were made at 1.0 and 0.1mg/ml. USP potency for both drugs were measured, cross referenced against US pharmacopiel standard and expressed as units per milligram. Whole blood activated clotting time was measured in healthy human volunteers at graded concentrations of both drugs. Plasma based anticoagulant assays such as activated partial thromboplastin time (APTT) and thrombin time (TT) were measured. Protamine neutralization studies were also carried out in the different assays used.ResultsThe USP potency of sulodexide range from 90 – 105 U/mg whereas the porcine heparin exhibited a potency range of 180 – 200 U/mg as measured by the anti‐Xa activity. In the ACT assays USP potency adjusted sulodexide and heparin produced concentration dependent prolongation of this test which were comparable to heparin. Both the sulodexide and heparin produce concentration dependent anticoagulant effects in the APTT and TT assays. Protamine sulfate produced effective neutralization of the anticoagulant effects of both the sulodexide and heparin.ConclusionsThese results suggest that at USP potency equated levels sulodexide is capable of producing similar anticoagulant effects as unfractionated heparin. The USP potency of sulodexide can be adjusted at a comparable potency to porcine heparin to obtain comparable anticoagulant responses in the in vitro setting. Additional in vivo studies are warranted to compare the potency adjusted sulodexide with heparin.