bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Development of a Genomic Health Disparity Database and Analytic Tool
Authors: Hughley Raymond Welsey , Tripathi Shweta , Davis Mellissa , Yates Clayton 
Published: November 2023

Publically available datasets such as The Cancer Genome Atlas (TCGA) provides scientific investigators and clinicians access to multiple NGS applications of patients including exome sequencing, comparative genomic hybridization ‐arrays, DNA methylation arrays, RNA sequencing, and reverse protein phase arrays. Many tools are being developed to allow basic researchers and clinicians without bioinformatics training to envisage, ‐analyze and understand the data, however, at the moment there is no centralized location to obtain sequenced genomic data that permits analysis of cancer patients based on health disparities. Interestingly, genomic analysis tools such as Oncomine and KM plot do not provide ethnicity as search criteria. Whether, this is a lack of ethnicity obtained at during sample acquisition or lack of including in the study, the result is that very few dataset have racial information, limiting the large scale analyses due to insignificant sample populations.Therefore, we proposed to create a data base that combines genome sequenced information from multiple locations that include racial information. Additionally, we have developed analytical tools to access files from databases like GSE files and the TCGA data, which contain information on race. Genes from each study where identified using David or the direct probe sequence information for each sequencing machine. R statistical language and multiple packages where used to normalize data sets and merge them into one centralized form. Ancestry markers (AIMS) and SNPs where used to verify ethnicity. We further developed analytic tools analyze Gene Expression and patient survival. The development of such a resource can greatly contribute in solving many of the health disparities questions being asked today and in the futureSupport or Funding InformationSupported by Department of Defense Prostate Cancer Research Program (PC120913) [CY], G12 RR03059–21A1 (NIH/RCMI) [CY], (NIH/NCI) 1 R21 CA188799–01, and a pilot project on U54 CA118623 (NIH/NCI) [CY]
Effects of Artemisia Annua leaf extract on hepatic steatosis and inflammation in high‐fat diet‐fed mice
Authors: Jeong Eun Ae , Kim Kyung Eun , Yi Chin‐ok , Lee Jong Youl , Roh Gu Seob 
Published: November 2023

Artemisia Annua L. (AA) is a well‐known source of the antimalarial drug artemisinin. AA also has an antibacterial and antioxidant activity. However, the effect of AA extract on hepatic steatosis induced by obesity is unclear. We investigated whether AA extract prevents obesity‐induced insulin resistance and hepatic steatosis in high‐fat diet (HFD)‐fed mice. Mice were randomly divided into groups that received a normal chow diet (ND) and HFD with or without AA for 12 weeks. We found that AA extract reduced insulin resistance and hepatic steatosis in HFD‐fed mice. Western blot analysis showed that HFD‐induced expression of nuclear sterol regulatory element‐binding protein 1 (SREBP1) and carbohydrate response element‐binding protein (ChREBP) in the livers was decreased by AA extract. In particular, dietary administration of AA extract decreased hepatic high‐mobility group box 1 (HMGB1) and cyclooxygenase‐2 (COX‐2) expression in HFD‐fed mice. AA extract also attenuated HFD‐induced collagen deposition and fibrosis‐related transforming growth factor (TGF)‐β1 and connective tissue growth factor (CTGF). These data indicate that dietary AA extract has beneficial effects on hepatic steatosis and inflammation in HFD‐fed mice.Support or Funding InformationNational Research Foundation of Korea (No.2014R1A2A1A11049588)
Nef mediated learning impairment is associated with a TGF‐β inflammatory environment in astrocyte cultures in vitro
Authors: Manoharan‐Valerio Michael Anand , Martinez‐Orengo Neysha , Noel Richard 
Published: November 2023

The worldwide epidemic of HIV has been ameliorated with the development of antiretroviral therapies. Modern treatment has been efficient in impairing viral replication, resulting in an undetectable viral load in patients. Unfortunately, the process of viral protein production is still functional contributing to detrimental conditions such as HIV associated neurocognitive disorders (HAND). Recent studies have associated HAND with astrocyte mediated toxicity of neurons, stimulating further investigations regarding the mechanisms of these effects. Studies conducted in our lab have shown loss of neurons and deficiency in the spatial learning of rats infused with astrocytes expressing the viral protein Nef. The release of inflammatory cytokines and modulation of TGF‐b pathway could be a plausible explanation for the pathology herein observed. We hypothesize that astrocytes transfected with Nef increase the expression of TGF‐b and promote the secretion of inflammatory cytokines. Therefore, we aim to investigate the possible molecular explanation to the relation between learning impairment, inflammation and modulation of TGF‐b pathway in the presence of HIV‐Nef. In order to verify the production of these factors, astrocytes were transfected by electroporation with a Nef or GFP plasmid. During the following 48 and 72 hours samples were collected and assessed by western blot and immunofluorescence. Resulting from these studies we found an increased expression of iNOS in supernantants and increased expression of TGF‐b in lysates of astrocytes expressing Nef compared to GFP controls. These results were more noticeable at 48 hours. We also observed that cellular localization of TGF‐b varied depending on treatment. In astrocytes transfected with GFP, TGF‐b labeling was primarily nuclear whereas in astrocytes transfected with Nef there was a distribution of the labeling more towards the cytoplasm. These results suggest a stimulation of a pro‐inflammatory environment by HIV‐Nef that could lead to harmful effects to neurons. We are also conducting in vitro co‐cultures of neurons exposed to astrocytes expressing Nef to study the extent of the inflammation and toxicity in this environment. Because TGF‐b can be either beneficial or negative to cell processes and cell response can vary depending on the type of TGF‐b receptor, further studies include understanding more in depth activation of the pathway. Studies have shown that the production of TGF‐b ligand can correlate directly or inversely to the receptors. Thus we are interested in measuring SMADs proteins, expression of TGF‐b receptors, and include a TGF‐b receptor blocker to better understand the role of this pathway.Support or Funding InformationR25GM082406, GM106970, MD007579
Small molecule GCPII inhibitor ameliorates disease activity in murine models of IBD
Authors: Rais Rana , Jiang Weiwei , Wozniak Krystyna , Stathis Marigo , Rojas Camilo , Li Xuhang , Slusher Barbara 
Published: November 2023

BackgroundFolate Hydrolase 1 (FOLH1) gene encodes a type II transmembrane glycoprotein termed glutamate carboxypeptidase II (GCPII) that cleaves terminal glutamate moieties from the abundant neuropeptide N‐acetylated aspartate‐glutamate (NAAG) in nervous tissues and sequentially from folate poly‐γ‐glutamate in the gut. Recent gene‐profiling and immunohistological analyses have shown a selective and robust upregulation of FOLH1/GCPII mRNA and protein in the intestinal mucosa of patients with Crohn's disease.MethodsUsing a functional FOLH1/GCPII radioenzymatic assay, we first quantified the glutamate carboxypeptidase activity in normal and diseased mucosa of 31 surgical intestinal specimens from 20 subjects including healthy controls and patients with inflammatory bowel disease (IBD). Using two validated murine models of IBD ‐dextran sodium sulfate (DSS)‐induced and IL10−/− spontaneous colitis models ‐we next explored the therapeutic potential of chronic GCPII inhibition using the selective GCPII inhibitor 2‐PMPA (IC50=300 pM).ResultsWe report a robust 300–3,000% increase in FOLH1/GCPII enzymatic activity in the intestinal mucosa of patients with active IBD when compared to that in an uninvolved area of the same patients, or the intestine from healthy controls. In the DSS‐colitis model, daily 2‐PMPA inhibited the glutamate carboxypeptidase activity in the colonic mucosa by over 90% and significantly reduced the disease activity index. These findings were corroborated in FOLH1−/− mice which showed significant protection to DSS‐induced colitis compared to wild type mice. In the murine IL‐10−/− model of colitis, daily 2‐PMPA treatment also significantly reduced both macroscopic and microscopic disease severity.ConclusionsWe have demonstrated, for the first time, a robust upregulation of FOLH1/GCPII enzymatic activity in diseased mucosa from IBD patients and significant attenuation of IBD symptoms in murine models using a selective FOLH1/GCPII inhibitor and in FOLH1−/− mice. These data strongly implicate FOLH1/GCPII in the etiology of IBD, providing a new therapeutic target.Support or Funding InformationThis research was supported by NIH Grant RO1CA161056
The Virginia Tech Center for Drug Discovery and the Virginia Drug Discovery Consortium
Authors: Kingston David George Ian 
Published: November 2023

This poster presents the work of two Virginia‐based drug discovery centers.The Virginia Tech Center for Drug Discovery, or VTCDD, was established in 2011 to bring together the expertise of scientists from several different departments at Virginia Tech with the mission to continue the growth and advance the stature of the existing drug discovery and development programs of the university. It operates as a “virtual center” with a small screening laboratory and a modest budget, but it has been successful in catalyzing several research collaborations and increasing grant funding. Two VTCDD members have drugs in clinical trials based on earlier work, and other members have developed new drug formulations and new drug candidates. The presentation will summarize the work of several VTCDD members.The Virginia Drug Discovery Consortium (VDDC) is a new Consortium between the major research universities in Virginia, including the University of Virginia, Virginia Commonwealth University, Virginia Tech, and the Virginia Tech Carilion Research Institute. Its initial focus is on diseases of the brain, and it has planned a BrainRx Symposium in Richmond, Virginia, for May 23–24 to promote this collaborative research focus. Details of this Symposium will be presented.Support or Funding InformationSupport of VTCDD by the Fralin Institute for Life Sciences at Virginia Tech is gratefully acknowledged
Development of a multiplexed plasmonic nanoparticle‐based assay to identify inhibiters of HuR protein‐RNA binding
Authors: Yoshida George , He Jie , Gabanic Andrew , Sagle Laura , Tranter Michael 
Published: November 2023

IntroductionRNA binding proteins such as HuR are becoming recognized as potential mediators of cardiac physiology and pathology, but this class of proteins has traditionally been considered to be “un‐druggable” targets. Recent work from our laboratory using a cardiomyocyte‐specific HuR‐deficient mouse model has identified HuR as a novel therapeutic target for heart failure. Specifically, deletion of HuR preserves cardiac function and decreases pathological ventricular remodeling in a mouse model of heart failure. In order to identify novel HuR inhibitors, we are collaborating with the Sagle laboratory, which has significant expertise in localized surface plasmon resonance (LSPR) biosensing and recently developed a nanoparticle fabrication technique applicable to high‐throughput drug screening. Thus, the objective of this study is to adapt a multiplexed plasmonic nanoparticle platform developed by the Sagle laboratory for the development of a novel plasmonic nanoparticle‐based drug screening assay to identify small molecule inhibitors of HuR.Methods and ResultsGold nanoparticle arrays, 100 nm in diameter and 60 nm in height, were fabricated and thiolated DNA was covalently bound to the surface of the gold. Next, a single‐stranded RNA containing a HuR target binding site was hybridized to the nanoparticle‐bound DNA. We are then able to detect HuR protein binding to its target site within the RNA by observing a LSPR shift induced by the increased mass bound to the gold nanoparticle surface. For each step of the assembly, a significant LSPR absorbance shift was observed with the addition of DNA, RNA, and HuR protein to the nanoparticle surface. Importantly, we are able to quantitatively demonstrate a reversal of HuR‐RNA binding in the presence an experimental new inhibitor.ConclusionOur results describe a novel multiplexed plasmonic nanoparticle‐based assay suitable for high‐throughput screening of drug candidates to inhibit RNA binding proteins through a simple colorimetric (LSPR) detection method. Here we demonstrate the initial application of this approach to specifically screen for inhibitors of the RNA binding protein HuR, but this assay provides a flexible platform applicable to many RNA binding proteins by simply changing the RNA target sequence.
Functional and Transcriptional Interactions Between Regulator of G‐protein Signaling Protein 10 (RGS10) and Tumor Suppressor Proteins in Cancer Chemosensitization
Authors: Hooks Shelley , Alqinyah Mohammed , Webster Andrew , Sakamuro Daitoku 
Published: November 2023

Ovarian cancer is the deadliest gynecologic cancer, accounting for approximately 15,000 deaths per year. Chemotherapeutic drugs are initially very effective, but more than 80% of patients whose tumors initially respond to chemotherapeutics will relapse within two years with drug‐resistant, terminal disease. Understanding the molecular changes that ovarian cancer cells undergo to gain the ability to survive in the presence of DNA‐damaging chemotherapeutics is critical to develop therapies for chemoresistant cancers. Our studies are focused on the protein Regulator of G‐protein Signaling protein 10 (RGS10), which we have shown is critical in maintaining sensitivity to cisplatin‐induced cell death. Analysis of gene and protein expression in multiple ovarian cancer cell lines demonstrates that expression of RGS10 is suppressed during progression to chemoresistance. Further, we show that acute loss of RGS10 expression directly induces chemoresistance. RGS10 is a nucleo‐cytoplasmic protein with unknown nuclear functions. In order to define the mechanism of RGS10's role in chemoresistance, we probed the functional interaction between RGS10 and the nucleo‐cytoplamic tumor suppressor protein Bridging Integrator 1 protein (BIN1). Our results reveal a functional interaction between RGS10 and BIN1. The ability of BIN1 to regulate cell survival in the presence of cisplatin is partially reversed by normalizing RGS10 expression levels. The mechanism of suppression of RGS10 during chemoresistance is not fully understood, but includes recruitment of histone deacetylase enzymes. To explore upstream signaling that may trigger loss of RGS10 expression, we further determined if there exists an effect of BIN1 expression on RGS10 expression. Our results show that manipulation of BIN1 expression in cancer cells acutely regulates RGS10 expression. Together, our results suggest that the expression and function of RGS10, a novel regulator of ovarian cancer cell survival, is modulated by the established tumor suppressor protein BIN1. Ongoing work will further define the molecular mechanisms linking these two regulator proteins.Support or Funding InformationMarsha Rivkin Center for Ovarian Cancer Research (SBH)NCI R01CA140379 (DS)
Liver lipid profiling of chemical‐induced phospholipidosis
Authors: Saito Kosuke , Ishikawa Masaki , Yamada Hiroshi , Nakatsu Noriyuki , Maekawa Keiko , Saito Yoshiro 
Published: November 2023

Lipids play important roles in multiple biological processes and its disorder is well associated with diseases and injuries. Thus, lipid profiling would be a useful to understand pathophysiology of but also to identify biomarker for chemical‐induced phospholipidosis. In the present study, we used rat model to overview liver lipid profiles of two types of phospholipidosis. Hepatic phospholipidosis were induced by treatment of clomipramine (CPM), imipramine (IMI), amitriptyline (AMT) and ketoconazole (KC) for 28 days. Phospholipidosis were determined by histopathological evaluation. CPM, IMI and AMT induced phospholipidosis in hepatocyte, while KC induced phospholipidosis in bile duct. To overview liver lipid profiles, we employed recently developed lipidomics platform with liquid chromatography and mass spectrometry (LC/MS), whic hsimultaneously determine the levels of broad spectrum of lipids. In total, we determined and examined 138 lipids (62 phospholipids, 10 sphingolipids and 65 neutral lipids). Each chemical treatment have their corresponding control treated with vehicle. To identify specific lipid alterations in the liver, we employed multivariate orthogonal partial least squares discriminant analysis. A bis‐monophosphatidic acid (BMP) (BMP[44:12]) and several triacylglycerols (TGs) were identified as specific lipids separating control and chemical‐treated rats in all models of phospholipidosis in the liver. The levels of BMP(44:12) were increased in the liver by chemical‐induced phospholipidosis. On the other hand, several TGs were increased in the liver by CPM, IMI and AMT but decreased by KC. Therefore, increased levels of BMP is common features of hepatic phospholipidosis and alteration of TGs might be associated with zone‐specific events in the liver. Our study provides the new insight into the alteration of liver lipidprofiles which probably reflecting chemical‐induced hepatic phospholipidosis and may help to understand its pathophysiology.Support or Funding InformationThis work was supported by the intramural research grant of National Institute of Health Sciences and the Health and Labour Sciences Research Grants (Grantnumber H028) from the Ministry of Health, Labour and Welfate of Japan.
The New Algorithm For Calculation Of Median Lethal Dose (Ld50) And Effective Dose Fifty (Ed50) Of Micrarus Fulvius Venom And Anti‐Venom Using Mice
Authors: Saganuwan Saganuwan Alhaji 
Published: November 2023

BackgroundOne million people throughout the world are bitten each year by poisonous snakes. Of this, one‐tenth died and three‐tenth suffer some forms of disabilities. In view of this, anti‐snake venoms are currently being developed against viper and colubrid snake venoms using mice. Therefore, a new algorithm for calculation of median lethal dose (LD50) and effective dose fifty (ED50) was developed for Micrarus fulvius venom and antivenom respectively.MethodsTherefore, this paper compared the formula of Effective Dose Fifty (ED‐50) developed by Spearman and Karber with ideal median lethal dose (IMLD‐50) formula developed by Saganuwan with a view to bringing out their difference and similarity in calculation of ED‐50 that could be used to develop a new median lethal dose formula for calculation of Micrarus fulvius venom in mice. To achieve this, various reported antivenom concentrations (17.2, 8.6, 4.3, 21.5 and 5.3 milligram per 20‐gram body of mice) were used for calculation of LD50 and ED50 of the snake venom and antivenom respectively.ResultThe LD50 value of coral snake venom using the new formula was 0.29 mg/kg body weight of mice whereas the ED50 was 428.75 mg/kg body weight respectively. The findings revealed that ED50 value (477 mg/kg) from Spearman and Karber's formula (ED50 = (logf()ED)_50 = (logf()X)_100 ‐ logf()FD/n (·t ‐ n/2)) is comparatively similar with ideal median lethal dose value (428.75 mg/kg) from Saganuwan's formula (MLD50 + MSD50/2). The new LD50 formula (LD50 = ((ED)_50/3) × Wm × 10‐4) yielded value (0.29 mg/kg) of comparative significance with reported value (0.32 mg/kg). When ED50 is equal to 2LD50, the denominator of (ED)_50/3 becomes 2.ConclusionIdeal median lethal dose formula of Saganuwan can be used to calculate an effective dose of Micrarus fulvius anti‐snake venom whereas the new median lethal dose formula can be used to calculate a dose of the snake venom that can kill 50% of test mice.Support or Funding InformationThis study was funded using my monthly salaries
The effect of antibiotics on the mitochondrial function in rat skeletal muscle
Authors: Morina Edon 
Published: November 2023

BackgroundMitochondria are the main energy producing organelle of the cell through oxidative phosphorylation (OXPHOS) and the electron transport system, and major sources of reactive oxygen species (ROS) result from superoxide (O2−) and hydrogen peroxide (H2O2). Accumulation of ROS has the potential to harm macromolecules such as DNA and RNA. How antibiotics contribute to oxidative damage in cells have not been sufficiently investigated, although Kohanski et al. (1) have proposed a mechanism of how bactericidal antibiotics increases O2− production causing an excessive production of hydroxyl radical (OH−) via the Fenton reaction. This study has therefore investigated the effect of clarithromycin, trimethoprim and penicillin on the mitochondrial respiration and H202 production in rat skeletal muscle to see if our findings correlate with Kohanski's proposal.MethodAn approach combining high‐resolution respirometry and fluorometric measurement of H2O2 production by the Oroboros Oxygraph 2K instrument was used. Skeletal muscle tissue from mice (C57BL/6JRJ) was prepared and permeabilized using saponin stock solution. A stepwise multiple substrate‐uncoupler‐inhibitor titration (SUIT) protocol was used to analyze the oxidative phosphorylation, the mitochondrial respiratory control, and H2O2 production. The drug concentrations of antibiotics were equivalent to those from clinical use. 6 muscle samples were exposed to each antibiotic and 6 were used as control. The software Datlab was used to calculate mitochondrial oxygen flux per mass [pmol/(s*mg)] and the H2O2 production using a fluorescent probe.ResultsOur findings showed that clinical doses of clarithromycin increased the mitochondrial respiration by 3.62 pmol, SD= ±4.71 compared to control which showed a decrease in respiration by −0.84 pmol, SD= ±1.16 (p‐value = 0.063). There were not observed any significant alterations in H202 production with the addition of clarithromycin as the H2O2 production increased by 0.52 pmol, SD= ±0.75 compared to control 0.011 pmol, SD= ±0.037 (p‐value = 0.164). Trimethoprim and penicillin on the other hand caused a decrease in mitochondrial respiration by −1.11 pmol SD= ±3.01 and −4.65 pmol SD= ±25.09 compared to their respective control −0.46 pmol SD= ±1.27 and 3.46 pmol SD= ±5.38, (p‐value = 0.706). No significant findings were observed with the H2O2 production.ConclusionOur findings suggest that clarithromycin possibly increases the mitochondrial respiration and leads to an increased production of O2−. Clarithromycin did increase the H202 production slightly. This study does not finally elucidate that antibiotics contribute to the formation of ROS, but can on the other hand assist the further understanding of drugs and mitochondrial dysfunction.Support or Funding InformationEdon Morina1, Vanja Cejvanovic1, Laura Kofoed Kjær1, Henrik Enghusen Poulsen1, Søren Nielsen21Q7642, Department of Clinical Pharmacology, Bispebjerg Hospital; 2Department of Health Science and Technology Aalborg University