bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Functional Validation of the miRNAs and their Targets, which are Essential to the Induction of Neointimal Hyperplasia
Authors: Kim Yerin
Published: April 2020

Angioplasty and stent procedures for widening the narrowed artery of atherosclerosis can cause restenosis by damaging endothelial cells. The main reason for this phenomenon is the migration and proliferation of vascular smooth muscle cells toward the intimal layer, which is called neointimal hyperplasia. After the function of miRNA, which is cell‐specific and fine‐tunes the translation of several mRNA targets, was known, several studies have identified miRNAs that affect arterial restenosis to overcome the limits of the previous drugs. However, most of the studies focused on one miRNA each. Therefore, it is necessary to ensure which of the individually studied miRNAs play a more important role at the beginning of restenosis. We should also ensure that there are any unknown miRNAs associated with restenosis regulation. In this study, we used the rat balloon injured carotid artery model to identify the entire differentially expressed (DE)‐miRNAs and DE‐mRNAs in the early stages of restenosis, through small RNA sequencing and total RNA sequencing, respectively. Among the DE‐miRNAs which show the same results in small RNA sequencing and RT‐qPCR, we focus on the rat, human conserved miRNAs with the largest change in expression (> 5 fold). The conserved DE‐miRNAs included previously well‐known miRNAs, such as miR‐221 and miR‐21, but also miRNAs, which show more change in expression but still unknown. By performing in vivo and in vitro functional assays, we were able to identify several undiscovered miRNAs that are effective in the cellular functions associated with the suppression of neointimal hyperplasia. Next, among the DE‐mRNAs identified by total RNA sequencing, we selected the predicted targets of the miRNAs through the target prediction databases (Targetscan, miRDB, miRmap). Also, we selected mRNAs functionally in context with the miRNAs by using the Gene Ontology (GO) term of the expected targets. We used RT‐qPCR to double‐check the changes in expression of these filtered targets and to confirm whether these predicted targets are actual targets for miRNAs. For the mRNA with the greatest variation, we performed luciferase assay to check whether the mRNA is a direct target of the miRNA. Additional functional assays were used to determine whether the target mRNA plays a central role in the progression of the neointimal hyperplasia.

In summary, we identified entire miRNAs and their target mRNAs that are important for restenosis control. Through this study, we expect to utilize diverse miRNAs for the diagnosis and therapy of restenosis.

Support or Funding Information

This study was supported by the grant from the National Research Foundation of Korea (2018029571)
Quantitative Proteomic Profile of Caribbean Hispanics with Resistance to Clopidogrel
Authors: Santiago-Cartagena Ednalise , Cantres Yadira , Carrasquillo Kelvin , Moneró Mariangeli , Meléndez Loyda , Roche Abiel , Duconge Jorge
Published: April 2020

The resistance to clopidogrel increases the risk of ischemic events in adults with coronary artery disease. This resistance varies with ethnicity, genetic, and many other clinical variables. Proteomic data from studies on Caribbean Hispanic (CH) patients treated with clopidogrel that have developed resistance has not yet been conducted. Thus, this is the first study performed on patients from the Caribbean region that also uses a cutting‐edge proteomic approach to a Precision Medicine application. A 10‐plex tandem mass tag labeling quantitative proteomic analysis was performed on plasma proteins isolated from CH patients treated with clopidogrel. Plasma samples from 6 patients were divided into two groups: non‐responder (High P2Y12 reaction units (PRU) ≥230) and responder (Low PRU <230). Both groups were compared with cardiovascular patients under other treatments. A total of 201 proteins were identified in the plasma. For the non‐responder group, 74 proteins were significantly down‐regulated, and 22 proteins were up‐regulated. Conversely, 55 proteins were significantly down‐regulated, whereas 28 proteins were up‐regulated in the responder group. Bioinformatic analysis showed that 8 of the regulated proteins were associated to the blood coagulation system pathway, and 5 proteins were associated with Intrinsic prothrombin activation pathway. Also, some of the significantly regulated proteins participate in two interaction networks associated with Acute coronary syndrome and Acute myocardial infarction. The proteomic analysis demonstrates differences in protein abundance regarding clopidogrel responses. These findings are expected to provide preliminary evidence on early expression of novel biomarkers in CH cardiovascular patients with resistance to clopidogrel.

Support or Funding Information

This study was supported by grant # 2U54 MD007600‐31 and Research Supplement to Promote Diversity in Health‐Related Research from NIMHD, NIH (CCRHD‐RCMI Program at UPR MSC).
Cardiovascular Effects of Three Distinct Anesthetic Approaches in Rats
Authors: Barboza Amanda Rosanna Alves , Silva Luiz Eduardo Virgílio , Salgado Helio Cesar , Jr Rubens Fazan
Published: April 2020

It is well known that anesthesia affects hemodynamics and leads to marked changes in neurohumoral modulation of the cardiovascular system, affecting results obtained in research protocols conducted during anesthesia. We evaluated the effect of three distinct anesthetic agents on arterial pressure (AP), heart rate (HR), and their variability indexes before and during anesthesia in rats. Conscious freely moving Wistar rats, previously instrumented with catheters in the femoral artery, had their AP recorded during 30 min. Following they were anesthetized with ketamine/xylazine (KX: 50/10 mg/kg, ip, N=7), urethane (URE: 1 g/kg, ip, N=7) or inhalation of isoflurane (ISO: 3–5%, N=10) and the AP recording was maintained for the next 30 min. At the onset of anesthesia with KX, the animals showed a marked rise in AP (D 47±2 mmHg) that slowly returned to normal values within 30 min. URE did not affect AP, while ISO caused a pressure drop of 16±1 mmHg. Overall blood pressure variability, measured by the standard deviation of systolic pressure values, was reduced during anesthesia with KX (D ‐ 1.9±0.5 mmHg) or URE (D −2.3±0.3 mmHg) but was not affected by inhalation of ISO. Likewise, the power of systolic AP spectra, an index of sympathetic vascular modulation, was markedly decreased by anesthesia with KX or URE (D −6.6±1.3 and −4.7±0.6 mmHg2, respectively) but not with ISO. Bradycardia (D −64±10 bpm) and an increase in HR (D 85±12 bpm) were caused by anesthesia with KX and URE, respectively. Inhalation of ISO had no effect on HR. Overall HR variability, measured by the standard deviation of normal cardiac intervals (SDNN), was markedly reduced by all anesthetic agents studied (D −1.1 to −2.0 ms for the three agents used). Spectral analysis showed that low‐frequency power of pulse interval (PI) spectra was decreased during anesthesia with KX (D −10±1 nu) or URE (D −11±3 nu). At the same time, it was not affected by the inhalation of ISO. The high‐frequency power of PI spectra was found reduced during anesthesia with the tree agents used (D −7.7 to −3.1 ms2). Multiscale entropy, an index of complexity of HR variability, showed that anesthesia with KX or URE, but not with ISO, decreased HR complexity at lower scales (1–6). At higher scales (7–20) entropy was markedly decreased by the three anesthetic agents studied. Our results revealed that, despite its hemodynamical effects, anesthesia decreases cardiovascular modulation. However, the inhalation of ISO is the anesthetic approach that preserves the most the characteristics of AP and HR variability, suggesting that this is the anesthesia that has less effect on cardiac and vascular modulation.

Support or Funding Information

Supported by FAPESP and CNPq
The Alterations of Blood Glucose and Cognitive Function by Ketone Injection in Mice
Authors: Cha Hee Yun , Yang Soo Jin
Published: April 2020

Objectives

The ketogenic diet is defined as a high‐fat and low‐carbohydrate diet, and has been applied to patients with epilepsy, cancer, dementia and obesity. Mounting evidence suggests that ketogenic diet has an anorexigenic effect regulating carbohydrate metabolism and protecting brain function. However, the effects of ketogenic diet have not been clearly proved. This experiment aimed to examine whether ketone injection affects body weight, food intake, glycemic control and cognitive function in mice.

Methods

ICR male mice (11 weeks of age) were assigned to either control group or ketone group. β‐hydroxybutyrate (BHB, 300 mg/kg/day) was intraperitoneal injected to ketone group mice for 28 days. After ketone treatment for 28 days, oral glucose tolerance test and nest building test of hippocampus function were performed, and then sacrificed. The serum BHB concentrations were measured using a BHB colorimetric assay kit.

Results

With the ketone injection, daily food intake and body weight changes were similar between groups. The weights of kidney were significantly increased by 28 days of ketone injection (P = 0.004), whereas, lung (P = 0.014) and spleen (P = 0.046) weights of ketone injection group were significantly lower in comparison with control group. The blood glucose concentrations at 2 hours after a glucose challenge were significantly increased by ketone injection (P = 0.045). During the nest building test, the control group mice barely touched cotton pad, and the untorn pad weights had a tendency to be high in control group mice.

Conclusions

In this experiment, ketone injection altered glycemic control after a glucose challenge, and might improve hippocampus function. Collectively, findings of current experiment indicate that ketogenic diet could be beneficial for maintaining cognitive function.
Tools to Find Glycoproteins in the Protein Data Bank and Generate Realistic 3D Structures for Them
Authors: Woods Robert J. , Montgomery David W. , Young Jasmine , Grant Oliver C. , Wentworth Daniel , Foley B. Lachele
Published: April 2020

With over 150,000 entries, the worldwide protein data bank (PDB) is the primary repository for 3D macromolecular structure. Unfortunately, structural, annotational, and ambiguity errors exist for carbohydrates throughout the database due in part to the lack of carbohydrate‐specific tools for checking the quality of structures prior to deposition. Our group has partnered with the PDB Biocuration team to assist in the identification and remediation of carbohydrates in their database and we have developed a user‐friendly web interface called GlyFinder to accurately find, retrieve, and assess these glycan and glycoproteins.

Using GlyFinder, we have found that 45,852 of the PDB entries contain carbohydrates (30.1% of the PDB). Nearly 6,000 glycoproteins have been identified, with an average of five N‐linked glycans per glycoprotein. Only 415 glycoproteins contained O‐linked glycans, with an average of three O‐linked glycans each. A surprisingly high number of glycoprotein PDBs (500, 7.45%) contain one or more N‐linked glycans that are alpha‐linked to the asparagine, illustrating the unfortunate errors that sometimes exist in the data.

Because of such errors, and because the glycans in crystal structures are often truncated, we have also developed tools (Glycoprotein Builder) that can build realistic models of the glycoprotein with intact glycans employing the crystal structure of the protein core. These models allow us to predict the impact of glycosylation on protein function, antigenicity, immunogenicity and stability. We illustrate these capabilities for several proteins, including human Erythropoietin, HIV gp120, and influenza A hemagglutinin.

Support or Funding Information

Support from NIH U01CA221216, U01GM125267, and P41GM103390
Effects of Moderate Ethanol Consumption with a n‐3 Diet on Lipid Profile and Liver Function in Mice
Authors: Giltvedt Kristine G. , Voutour Luciano , Tursellino Brianna , Zella Alexandra , Brasser Susan M. , Hong Mee Young
Published: April 2020

Several studies have found a non‐linear relationship between alcohol consumption and cardiovascular disease (CVD) risk, suggesting that low or moderate consumption of alcohol may provide cardioprotective effects, while excessive alcohol consumption increases the risk of CVD. Studies also suggest that increased dietary consumption of n‐3 fatty acids may reduce CVD risk. The purpose of this study is to examine the effects of moderate ethanol consumption as a function of dietary n‐6:n‐3 fatty acid composition on markers associated with cardiovascular disease and liver dysfunction in mice. Twenty‐three mice (12 male, 11 female) consumed an 18% ethanol solution or 26.9% maltose dextrin solution (non‐ethanol isocaloric control) for 12 weeks. In each group, half of the mice were fed either a high n‐6 (n‐6:n‐3 = 50:1) diet or a balanced n‐3 (n‐6:n‐3 = 1:1) diet ad libitum. There were no differences in initial body weight between the two groups; however, the control group gained significantly more weight than the ethanol group (P = 0.020) associated with higher maltose dextrin fluid intake (P < 0.001). In the control group, the balanced n‐3 diet resulted in significantly lower aspartate aminotransferase (AST) levels (P = 0.010) compared to the high n‐6 diet. In the ethanol group, the balanced n‐3 diet resulted in lower levels of serum triglycerides (P = 0.086), total cholesterol (P= 0.096), and low‐density lipoprotein (LDL) levels (P = 0.053) that were approaching significance. These findings indicate that a diet with a balanced n‐6 to n‐3 ratio may improve several lipid profile markers associated with CVD in mice who concurrently consume moderate amounts of alcohol.

Support or Funding Information

NIH AA023291
Quantitative Histopathological Analysis of a Diet‐Induced NASH Mouse Model Using Artificial Intelligence
Authors: Schroen Daniel , Sanchez Marisa , Kelly Susan , MacBride Megan , Richardson Janell , Singh Manindra , Wilkinson Brandy , Catania Sara Becker
Published: April 2020

Non‐alcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease. It results in an accumulation of fat in the liver, and can progress to a more pathologically significant form of NAFLD known as non‐alcoholic steatohepatitis (NASH). Patients with NAFLD and NASH present on a spectrum of the disease, characterized by hepatitis (inflammation) and hepatocellular ballooning (cellular injury), which can lead to excessive fibrosis and scarring. Currently, diagnosis is confirmed by liver biopsies that are qualitatively analyzed by experienced pathologists who assign scores for each feature. However, documented inter‐pathologist variability in scoring and the semi‐quantitative nature of the scoring system itself highlight the need for new methods to differentiate NAFLD and NASH, and ensure the unbiased, consistent assessment of disease to better diagnose and stratify patients for treatment options. To support this effort we developed imageDx™: NASH, a collection of artificial intelligence (AI)‐based pathology models, to histopathologically validate and characterize NASH in a novel Diet Induced NASH BL6 Model. Livers from mice on a NASH‐inducing diet and a control diet were processed, sectioned, stained and digitally scanned to generate whole slide images. Quantification of each of the pathological features in mice was performed using imageDx™: NASH, including steatosis (macro‐ and micro‐vesicular), inflammation, hepatocellular ballooning/degeneration, fibrosis and the presence of Mallory bodies. These validated machine learning algorithms were developed with input from experienced pathologists with the goal of providing a more informative analysis of the pathology. The AI‐generated results were compared with semi‐quantitative scores provided by a board‐certified doctor of veterinary medicine. Using this diet‐induced NASH rodent model both with and without therapeutic interventions, these algorithms effectively identified small differences in tissue morphology that may not be easily discernible by visual examination. By developing highly reproducible and sensitive computational models, this study provides a foundation for a better understanding of disease mechanism and the development of effective therapeutics for NASH.
Acute Vascular Responses to All‐Extremity Aerobic Exercise
Authors: Lim Jisok , Holmer Brady , Lapierre Stephanie , Hwang Chueh-Lung , Sakarya Yasemin , Handberg Eileen M. , Schwartz Cody , Bhattal Gurjaspreet , Maharrey Phillip , Christou Demetra D.
Published: April 2020

Endothelial function and central arterial stiffness are independent predictors of future cardiovascular events. High‐intensity interval training (HIIT) is a popular and oftentimes superior exercise strategy for decreasing cardiovascular disease risk than moderate‐intensity continuous training (MICT). We have recently adapted HIIT on a non‐weight‐bearing all‐extremity ergometer to reduce impact on the joints and involve muscles in the whole body to activate a larger amount of muscle mass than in lower‐extremity HIIT. However, the acute vascular responses to all‐extremity HIIT and MICT remain unexplored and may be important for optimizing exercise prescription. Therefore, the purpose of this study was to investigate the acute effects of all‐extremity HIIT and MICT on endothelial function, central arterial stiffness and hemodynamics. Sixteen young men (21±1 years of age, means±SE) who were free of clinical disease and did not use tobacco products or medications participated in this study. Vascular measures were assessed at pre‐exercise, at the end of a single session of HIIT and MICT and following recovery. HIIT and MICT were matched for caloric expenditure and were performed on an all‐extremity non‐weight‐bearing ergometer, at least one week apart. HIIT consisted of 4×4‐min intervals at 90% peak heart rate (HRpeak) interspersed by 3‐min intervals at 70% HRpeak for a total of 40 min. MICT consisted of 47 min at 70% HRpeak. Endothelial function was assessed using brachial artery flow‐mediated dilation (FMD) via high resolution ultrasonography in response to 5 min forearm blood flow occlusion. Arterial stiffness (carotid to femoral pulse wave velocity; cfPWV), aortic wave reflection (augmentation index normalized at heart rate 75; AIx75) and aortic systolic and diastolic blood pressure (aoSBP and aoDBP) were assessed using a validated cuff‐based device. HIIT did not result in significant changes in FMD (P=0.08), cfPWV (P=0.3), aoSBP (P=0.1) or aoDBP (P=0.2) within one hour from exercise cessation. AIx75 and heart rate were increased at the end of HIIT and remained elevated following recovery (P≤0.002 vs. pre‐exercise). In response to MICT, FMD remained unchanged (P=0.1). However, cfPWV decreased at the end of MICT (P=0.003) and returned to the pre‐exercise level following recovery (P=0.5). AIx75 increased at the end of MICT (P<0.0001) and returned to the pre‐exercise level following recovery (P=0.3). aoSBP decreased following recovery compared with end of MICT (P=0.04), but was not different than the pre‐exercise level (P=0.3). aoDBP did not significantly change in response to MICT (P=0.09). In conclusion, all‐extremity HIIT and MICT did not attenuate endothelial function or result in adverse changes in aortic blood pressure. MICT, but not HIIT, slightly reduced central arterial stiffness. These findings may have important implications for exercise prescription.
The Efficacy of Cola acuminata on Gram‐Negative Bacteria
Authors: Telles Caroline , McKinsey Cayla
Published: April 2020

Traditional healers have long used plant‐derived products to prevent or cure infectious diseases. The main reason is that these natural products may contain antimicrobial agents that are effective against drug‐resistant bacteria. The Bizzy nut is a “cure‐all” herbal medicine that is useful for many medical purposes, such as removal of poisons from the body; birth control; control of diabetes; weight loss; and contains antimicrobial activity. Previously, we reported on the antimicrobial property of the natural product, Bizzy nut, in gram‐positive bacteria. In this study, we extended this analysis to gram‐negative organisms. The antimicrobial activity of an acetone extract (Biz‐3) of Bizzy nut was determined using the agar well diffusion method and the MIC assay. We observed that a concentration between 30ug/mL to 50ug/mL Bizzy nut was effective in killing gram‐negative organisms. Our data demonstrate that gram‐positive organisms, such as Staphylococcus aureus, was 5–6‐times more potent towards the Bizzy nut extract. The order of potency of the organisms examined is Klebsiella pneumoniae > Escherichia coli > Enterobacter aerogenes. This study suggests that Bizzy nut contains selective antimicrobial activity.
NEGR1 may associate with a cluster of differentiation 36 (CD36) protein
Authors: YOO ARA
Published: April 2020

NEGR1 (Neuronal growth regulator 1) is a newly‐identified obesity‐related gene which was initially documented as a commonly down‐regulated gene from various tumor biopsies. Previously, we reported a new role of NEGR1 in cholesterol trafficking by revealing the interaction with a Niemann‐Pick diseases, type C2 (NPC2) protein. Also, intracellular lipid content increased in NEGR1‐deficient cells. In this study, we identified that the transcriptional level of CD36 significantly decreased in NEGR1−/− mouse embryo fibroblast cells. CD36 is a member of the class B scavenger receptor family of cell surface proteins that function in imports of fatty acids across membrane. Subsequent in vivo immunoprecipitation revealed that NEGR1 associates with CD36. Domain analysis revealed that two separate regions of CD36 are important for NEGR1 binding. Altogether, we suggest that NEGR1 may be involved in the regulation of intracellular fatty acid transport by interacting with CD36.

Support or Funding Information

Korea Research Foundation
Group Housing of Male Mice Causes a Significant Decrease in Circadian Rhythms and are indicative of Hypertension and Cardiovascular Disease.
Authors: Brown Nina , Sampson Austin , Richardson Kimberlei , Lee Dexter L.
Published: April 2020

Changes in day ‐ night time mean arterial pressure (MAP) predict hypertension and cardiovascular diseases. When there is a decrease in day ‐ night time MAP changes, the chances of hypertension and cardiovascular diseases increase significantly. Our hypothesis is that socialization of male mice causes a decrease in the day ‐ night time changes in MAP and heart rate (HR). Male mice, 6 – 8 weeks of age, were implanted with a biotelemetry device from Data Sciences (male mouse in a single cage) or TSE (multiple male mice in a single cage). Day and Night MAP for Data Science mice were 131 ± 0.5 and 157 ± 1.5 mmHg, respectively. Day and Night MAP for TSE mice were 114 ±7.0 and 124 ± 3.6 mmHg, respectively. The change in day and night MAP were 26 ± 2.2 mmHg in Data Science and 8.4 ± 4.0 mmHg in TSE mice. Day and Night time HR for Data Science mice were 482 ± 6 bpm and 505 ± 5.4 bpm, respectively. The change in day and night time HR were 36 ± 6 bpm in Data Science and 51 ± 12 bpm in TSE mice. Data Science mice had a higher MAP than TSE mice, the change in day ‐ night time MAP was less than TSE mice. The change in day and night time HR was also less in Data Science mice. Therefore, socialization of mice decreases day to night change in MAP and are indicative of hypertension and cardiovascular diseases.

Support or Funding Information

Funding:‐National Institute of Aging Grant (R25). Principal Investigators: Dr. Atanu Duttaroy and Dr. Kebreten Manaye, Howard University ‐National Institutes of Health: 5K01HL092593‐05, Principal Investigator: Dr. Dexter L. Lee‐The Leadership Alliance, Brown University
Food with Specialized Dietary Fiber Sources Improves Clinical Outcomes in Adult Cats with Constipation or Diarrhea
Authors: Wernimont Susan M. , Fritsch Dale A. , Schiefelbein Heidi M. , Brejda John J. , Gross Kathy L.
Published: April 2020

Changes in gastrointestinal (GI) microbiome composition and metabolism have been identified in many patients with gastrointestinal diseases, and the GI microbiome may play an important role in promoting and maintaining GI health. This study evaluated the efficacy of a fiber‐supplemented Control Food (CF) and a therapeutic food (TF) with specialized plant fibers known to contain antioxidant and polyphenol compounds in cats with constipation or diarrhea. A prospective clinical study was conducted with 44 adult cats, recruited from private veterinary practices across the United States. Cats exhibiting clinical signs of diarrhea or constipation were enrolled in the study. Cats were excluded from this study if they were under 1 year of age, had systemic disease including kidney disease (IRIS stage 3 or greater), had a Body Fat Index less than 20, were unwilling or unable to exclusively consume the study food, had megacolon or were otherwise unlikely to benefit from a fiber supplemented food, chronically used colonic motility drugs, or were currently receiving oral antibiotics or probiotics and were unwilling to discontinue. Enrolled cats were randomized to one of two complete and balanced dry therapeutic foods (25 CF, 19 TF). Fiber sources included CF: cracked pearled barley, ground whole grain corn, dried beet pulp, fructooligosaccharides (FOS) & psyllium seed husk; TF: ground whole grain corn, ground pecan shells, cracked pearled barley, whole grain oats, dried beet pulp, pea fiber, flaxseed, dried citrus pulp, pumpkin, pressed cranberries, FOS & psyllium seed husk. Veterinarians performed physical examinations, evaluated clinical signs of constipation or diarrhea and rated the cat’s response to the study food at days 2, 3, 4, and 28 using a defined scale (Negative Response, Non‐Response, Positive Response, and Complete Response). This study was reviewed & approved by the Institutional Animal Care & Use Committee, Hill’s Pet Nutrition, Inc. Veterinarian evaluations were analyzed using a Cochran‐Mantel‐Haenszel test with modified ridit scores. Results significant at p<0.05 are reported. The proportion of cats receiving CF rated by the veterinarian as Positive or Complete Response vs. study start was 36% at day 2, 48% at day 3, 60% at day 4, and 69% at day 28 (p=NS); the proportion of cats receiving TF rated by the veterinarian as Positive or Complete Response vs. study start was 42% at day 2, 63% at day 3, 65% at day 4, and 100% at day 28 (p<0.01). TF rapidly and effectively resolved veterinarian‐assessed clinical outcomes in cats with constipation or diarrhea. Fiber sources rich in antioxidant and anti‐inflammatory compounds were more effective than traditional fiber sources in improving clinical response in cats with diarrhea or constipation.

Support or Funding Information

This study was funded by Hill’s Pet Nutrition, Inc.
Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)
Authors: Zhang Gui , Lai Xin-He , Yang Jing , Jin Dong , Pu Ji , Xiong Yanwen , Yang Caixin , Dong Kui , Huang Ying , Luo Xuelian , Lu Shan , Xu Jianguo
Published: April 2020

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111T belong to the genus

Luteimonas

, and are closest to

Luteimonas rhizosphaerae

4-12T (98.02 % similarity),

Luteimonas aestuarii

B9T (97.8 %) and

Luteimonas terrae

THG-MD21T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111T and its closely related species was 83.34 %, well below the threshold of 95–96 %. The major cellular fatty acids were iso-C11 : 0, iso-C15 : 0 and iso-C17 : 1
 ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35–37 °C, pH 7.0–8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111T represent a novel species in genus

Luteimonas

, for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111T=DSM 104077T=CGMCC 1.16429T) is proposed.
Characterization and spontaneous induction of urinary tract Streptococcus anginosus prophages
Authors: Brassil Bridget , Mores Carine R. , Wolfe Alan J. , Putonti Catherine
Published: April 2020

Streptococcus anginosus

is an often overlooked and understudied emerging pathogen inhabiting many areas of the human body. Through our sequencing of

S. anginosus

strains isolated from the female bladder microbiota, we detected numerous prophage sequences. Bioinformatic analysis of these sequences identified 17 distinct groups of

S. anginosus

prophages. The majority of these phages exhibit no sequence homology to previously characterized temperate or virulent phage sequences, indicating an unexplored diversity of

Streptococcus

phages. By culturing these bacterial isolates, we confirmed that the prophages of five of these groups are capable of induction. One of these putative phages was imaged, the first such evidence of an

S

.

anginosus

virus-like particle; it exhibits morphological characteristics of siphoviruses.
The Melanoma Genomics Managing Your Risk Study randomised controlled trial: Statistical Analysis Plan
Authors: Lo Serigne N , Smit Amelia K , Espinoza David , Cust Anne E
Published: April 2020

Background

The Melanoma Genomics Managing Your Risk Study is a randomised controlled trial that aims to evaluate the efficacy of providing information on personal genomic risk of melanoma in reducing ultraviolet radiation (UV) exposure, stratified by traditional risk group (low or high phenotypic risk) in the general population. The primary outcome is objectively measured total daily Standard Erythemal Doses at 12 months. Secondary outcomes include UV exposure at specific time periods, self-reported sun protection and skin-examination behaviors, psychosocial outcomes, and ethical considerations surrounding offering genomic testing at a population level. A within-trial and modelled economic evaluation will be undertaken from an Australian health system perspective to assess the cost-effectiveness of the intervention.

Objective

To publish the pre-determined statistical analysis plan (SAP) before database lock and the start of analysis.

Methods

This SAP describes the data synthesis, analysis principles and statistical procedures for analysing the outcomes from this trial. The SAP was approved after closure of recruitment and before completion of patient follow-up. It outlines the planned primary analyses and a range of subgroup and sensitivity analyses. Health economic outcomes are not included in this plan but will be analysed separately. The SAP will be adhered to for the final data analysis of this trial to avoid potential analysis bias that may arise from knowledge of the outcome data.

Results

This SAP is consistent with best practice and will enable transparent reporting.

Conclusion

This SAP has been developed for the Melanoma Genomics Managing Your Risk Study and will be followed to ensure high-quality standards of internal validity and to minimise analysis bias.

Trial registration

Prospectively registered with the Australian New Zealand Clinical Trials Registry ACTRN12617000691347 (date registered: 15/05/2017).
SARS-COV-2 comorbidity network and outcome in hospitalized patients in Crema, Italy
Authors: Benelli Gianpaolo , Buscarini Elisabetta , Canetta Ciro , Piana Giuseppe La , Merli Guido , Scartabellati Alessandro , Viganò Giovanni , Sfogliarini Roberto , Melilli Giovanni , Assandri Roberto , Cazzato Daniele , Rossi Davide Sebastiano , Usai Susanna , Caldarelli Guido , Gili Tommaso , Tramacere Irene , Pellegata Germano , Lauria Giuseppe
Published: April 2020

No systematic data on hospitalized SARS-COV-2 patients from Western countries are available. We report onset, course, correlations with comorbidities, and diagnostic accuracy of nasopharyngeal swab in 539 individuals suspected to carry SARS-COV-2 admitted to the hospital of Crema, Italy. All individuals underwent clinical and laboratory exams, SARS-COV-2 reverse transcriptase-polymerase chain reaction on nasopharyngeal swab, and chest X-ray and/or computed tomography (CT). Data on onset, course, comorbidities, number of drugs including angiotensin converting enzyme (ACE) inhibitors and angiotensin-II-receptor antagonists (sartans), follow-up swab, pharmacological treatments, non-invasive respiratory support, ICU admission, and deaths were recorded. Among 411 SARS-COV-2 patients (66.6% males) median age was 70.5 years (range 1-99). Chest CT was performed in 317 (77.2%) and showed interstitial pneumonia in 304 (96%). Fatality rate was 17.5% (74% males), with 6.6% in 60-69 years old, 21.1% in 70-79 years old, 38.8% in 80-89 years old, and 83.3% above 90 years. No death occurred below 60 years. Non-invasive respiratory support rate was 27.2% and ICU admission 6.8%. Older age, cough and dyspnea at onset, hypertension, cardiovascular diseases, diabetes, renal insufficiency, >7 drugs intake and positive X-ray, low lymphocyte count, high C-reactive protein, aspartate aminotransferase and lactate dehydrogenase values, and low PO2 partial pressure with high lactate at arterial blood gas analysis at admission were significantly associated with death. Use of ACE inhibitors or sartans was not associated with outcomes. Comorbidity network analysis revealed homogenous distribution of deceased and 60-80 aged SARS-COV-2 patients across diseases. Among 128 swab negative patients at admission (63.3% males) median age was 67.7 years (range 1-98). Chest CT was performed in 87 (68%) and showed interstitial pneumonia in 76 (87.3%). Follow-up swab turned positive in 13 of 32 patients. Using chest CT at admission as gold standard on the entire study population of 539 patients, nasopharyngeal swab had 80% sensitivity. SARS-CoV-2 caused high mortality among patients older than 60 years and correlated with pre- existing multiorgan impairment. ACE inhibitors and sartans did not influence patients’ outcome.
Crowding and the epidemic intensity of COVID-19 transmission
Authors: Rader Benjamin , Nande Anjalika , Adlam Ben , Hill Alison L. , Reiner Robert C. , Pigott David M. , Gutierrez Bernardo ,   COVID-19 data working group, Brownstein John S. , Castro Marcia C. , Tian Huaiyu , Pybus Oliver G. , Scarpino Samuel V. , Kraemer Moritz UG
Published: April 2020

The COVID-19 pandemic is straining public health systems worldwide and major non-pharmaceutical interventions have been implemented to slow its spread1-4. During the initial phase of the outbreak the spread was primarily determined by human mobility5,6. Yet empirical evidence on the effect of key geographic factors on local epidemic spread is lacking7. We analyse highly-resolved spatial variables for cities in China together with case count data in order to investigate the role of climate, urbanization, and variation in interventions across China. Here we show that the epidemic intensity of COVID-19 is strongly shaped by crowding, such that epidemics in dense cities are more spread out through time, and denser cities have larger total incidence. Observed differences in epidemic intensity are well captured by a metapopulation model of COVID-19 that explicitly accounts for spatial hierarchies. Densely-populated cities worldwide may experience more prolonged epidemics. Whilst stringent interventions can shorten the time length of these local epidemics, although these may be difficult to implement in many affected settings.
Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater
Authors: Nemudryi Artem , Nemudraia Anna , Wiegand Tanner , Surya Kevin , Buyukyoruk Murat , Vanderwood Karl K , Wilkinson Royce , Wiedenheft Blake
Published: April 2020

SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 52-day time course. We show that changes in SARS-CoV-2 RNA concentrations correlate with local COVID-19 epidemiological data (R2=0.9), though detection in wastewater trails symptom onset dates by 5-8 days. We determine a near complete (98.5%) SARS-CoV-2 genome sequence from the wastewater and use phylogenic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for high-resolution genotyping of the predominant strains circulating in a community.
Combined use of absolutely quantitated cyclin D1 and Ki67 protein levels to improve prognosis of Luminal-like breast cancer
Authors: Hao Junmei , Zhang Wenfeng , Lv Yan , Zou Jiarui , Zhang Yunyun , Lv Jiahong , Xie Shuishan , Zhang Cuiping , Zhang Jiandi , Tang Fangrong
Published: April 2020

Purpose

Both Ki67 and cyclin D1 are routinely used protein biomarkers of cell proliferation for breast cancer patients. Ki67 is used to differentiate Luminal A-like from Luminal-B like subtype in surrogate assay. These two proliferative factors are investigated in this retrospective study to evaluate their prognostic role on the overall survival (OS) of Luminal-like breast cancer patients.

Method

The cyclin D1 protein level was measured absolutely and quantitatively using Quantitative Dot Blot (QDB) method in 143 Luminal-like FFPE breast cancer specimens. An optimized cutoff at 0.71 μmole/g was identified and used to separate these specimens into cyclin D1 high and low groups alone, or in combination with Ki67, for overall survival (OS) analyses of these patients.

Results

Cyclin D1 was found to be an independent prognostic factor from Ki67 in univariate and multivariate analysis. When both biomarkers were used to separate these Luminal-like specimens, the group with low expression of both biomarkers (n=52) had significantly improved 10 year survival probability at 94%, while the one with high expression of both markers (n=34) were at 41% based on Kaplan-Meier survival analysis of OS (Log rank test p<0.0001).

Conclusion

We demonstrated cyclin D1 as an independent prognostic protein biomarker from Ki67 for Luminal-like breast cancers. The combined usage of cyclin D1 and Ki67 significantly improved the prognosis over current prevailing surrogate assay. We propose to incorporate cyclin D1 in surrogate assay to improve prognosis for Luminal-like breast cancer patients in future clinical practice.
Feeding behaviour and its determinants among healthy toddlers in an urban city of India
Authors: Bhairavabhatla Kameswari C , Epari Venkatarao , Panigrahi Sandeep Kumar
Published: April 2020

Introduction

Growth and development of a child is largely influenced by feeding behaviour. Feeding problem in infancy and childhood is an important aspect since this may be associated with under-nutrition or even childhood obesity. Social, environmental and emotional factors, type and taste of food, perceptions and practices of parents, etc. may all determine feeding behaviour of child. This study tries to find out the proportion of normal toddlers presenting with feeding problem, factors associated with feeding behaviour and their association with physical growth among these toddlers.

Methods

A total of 100 mothers of 1 to 3 year-old children visiting for immunization were interviewed using systematic sampling method. A tool was developed by modifying existing tools are review of literature, was pre-tested and used. Association of various factors with eating behaviour and body mass index (BMI) were studied. Variables measured included perceived feeding problem, anthropometric measures, socio-demographic, emotional, environmental, parental factors, etc. Analysis was done using Chi-square test, t-test or Mann-Whitney U test using IBM SPSS v 20.0.

Results

Median age of the children was 19 months. 35% had a feeding problem. None of the socio-demographic variables were found to have any association with feeding problem. All children born preterm had eating problem. Feeding problem got undetected if fed by anyone other than mother. The mean TV viewing time for children with eating problem was significantly more (p = 0.017). Education status of mothers had a positive association with body mass index of the child (p=0.010). Anger, forced feeding and sleepy/drowsiness were reported to decrease feeding while happiness, caressing while feeding, semi-solid and liquid foods, eating with siblings and friends, and hearing short stories were reported to increase.

Conclusion

Feeding problem was present in 35% of the toddlers. Preterm birth, long hours of TV viewing during feeding, are associated with eating problem. Mothers are the best persons to identify this problem. Better maternal education decreases the burden of under nourished children though it increases those of overweight and obese.
Dynamic Behavior of Coupled Neuron System from a Game-Theoretic Standpoint
Authors: Kori Avinash
Published: April 2020

This paper is concerned with the theoretical investigation of game theory concepts in analyzing the behavior of dynamically coupled oscillators. Here, we claim that the coupling strength in any neuronal oscillators can be modeled as a game. We formulate the game to describe the effect of pure-strategy Nash equilibrium on two neuron systems of Hopf-oscillator and later demonstrate the application of the same assumptions and methods toN×Nneuronal sheet. We also demonstrate the effect of the proposed method on MNIST data to show the equilibrium behavior of neurons in aN×Nneuronal grid for all different digits. A significant outcome of the paper is a modified Hebbian algorithm, which adapts the coupling weights to neural potential resulting in a stable phase difference. Which in turn, makes it possible for an individual neuron to encode input information.
Ultrasound Monitoring of Descending Aortic Aneurysms and Dissections in Mice
Authors: Sawada Hisashi , Franklin Michael K. , Moorleghen Jessica J. , Howatt Deborah A. , Kukida Masayoshi , Lu Hong S. , Daugherty Alan
Published: April 2020

Several modalities, such as computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound, are available to visualize mouse aortas.1-3CT and MRI enable us to obtain reliable images of the aorta and its branches. However, CT requires vascular contrast and MRI is procedurally complex. Thus, these modalities are used only occasionally for in vivo monitoring of mouse studies. High frequency ultrasonography is a common approach for aortic monitoring in mice.4The standard ultrasound approach using a para-sternal view can visualize the aortic root, ascending aorta, and aortic arch, while this approach cannot visualize the descending region due to the presence of lungs and ribs. Therefore, the ability to perform in vivo monitoring of descending aortic diseases in mice has been an impediment. This study reports a para-spinal dorsal approach for ultrasound imaging of mouse descending aortas.
A Fast High-Affinity Fluorescent Serotonin Biosensor Engineered from a Tick Lipocalin
Authors: Zhang Shen , Li Xinyu , Drobizhev Mikhail , Ai Hui-wang
Published: April 2020

The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

Details

Regrettably, we, and several other researchers in the corresponding author’s lab and not involved in the original study, have been unable to reproduce some of the reported key results under conditions originally described.

We recently used the pDisplay-G-GESS-M plasmid to transfect HEK 293T cells and observed that the membrane localization of the biosensor was sensitive to FBS batches. By using an FBS batch from Gibco (Cat# 16000-044 and Lot #2103017RP), we were able to replicate the membrane localization similar to what was reported in Fig. 1e. However, the cells required the addition of several hundred micromolar of serotonin for robust fluorescence increase. These new results suggest that the affinity of G-GESS to serotonin is worse than that claimed in the initial article.

We further used liquid chromatography–mass spectrometry (LC–MS) to analyze the serotonin stock solutions identified in our −80°C lab freezer and observed MS peaks suggesting a glutamate contamination in some of the analyzed samples. In addition, we used polymerase chain reaction (PCR) or reverse transcription–PCR (RT–PCR) to amplify gene fragments from our viral stocks and the sequencing results indicate that the viral stocks were contaminated with a glutamate biosensor.

While we are still performing further investigation, in light of the existing findings, all authors agree to retract this paper.

In the initial article, the sensor was tested in several cell culture systems, brain slices and behaving mice. We are presently unable to fully explain the observed sensor responses described in the initial article, but it is highly possible that these responses could be caused by the contaminated chemical or viral stocks.

We deeply apologize to the scientific community for not detecting these problems sooner.
A systems pharmacology approach to determine the mechanisms of action of pleiotropic natural products in breast cancer from transcriptome data
Authors: Odongo Regan , Zergeroğlu Asuman Demiroğlu , Çakir Tunahan
Published: April 2020

Plant-derived compounds as natural products have attracted a lot of attention in the treatment of complex diseases, especially cancers, primarily due to their poly-pharmacologic mechanisms of action. However, methodological limitations have impeded gaining complete knowledge of their molecular targets. While most of the current understanding of these compounds is based on reductive methods, it is increasingly becoming clear that holistic techniques, leveraging current improvements in omic data collection and bioinformatics methods, are better suited for elucidating their systemic effects. Here, to provide an explanation to the mechanisms of action of plant-derived natural products in breast cancer, we applied a data integration approach to comprehensively study oncogenic signaling pathways targeted by withaferin A, actein, compound kushen injection and indole-3-carbinol. Specifically, we mapped the transcriptome-level response of cancer cell lines to these molecules on a human protein-protein interaction network and constructed the underlying active subnetworks. We used these subnetworks to define the perturbed signaling pathways and validated their relevance in carcinogenesis. The similarity of each identified oncogenic signaling pathway in terms of overlapping genes was subsequently used to construct pathway-pathway interaction networks, which were used to reduce pathway redundancy and to identify pathway crosstalk. Filtered pathways were then mapped on three major carcinogenesis processes. The results showed that the pleiotropic effects of plant-derived drugs at the gene expression level can be used to predict targeted pathways. Thus, from such pathways, it is possible to infer a systemic mechanism of action of such natural products.