Current Research on Non-Coding Ribonucleic Acid (RNA).

PubMed

Wang, Jing; Samuels, David C; Zhao, Shilin; Xiang, Yu; Zhao, Ying-Yong; Guo, Yan

2017-12-05

Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA. In small RNA, we discuss miRNA, transfer RNA, piwi-interacting RNA, small nucleolar RNA, small nuclear RNA, Y RNA, single recognition particle RNA, and 7SK RNA. We elaborate on the origin, detection method, and potential association with disease, putative functional mechanisms, and public resources for these non-coding RNAs. We aim to provide readers with a complete overview of non-coding RNAs and incite additional interest in non-coding RNA research.

Number of minimum-weight code words in a product code

NASA Technical Reports Server (NTRS)

Miller, R. L.

1978-01-01

Consideration is given to the number of minimum-weight code words in a product code. The code is considered as a tensor product of linear codes over a finite field. Complete theorems and proofs are presented.

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions

PubMed Central

Kumari, Pooja; Sampath, Karuna

2015-01-01

For many decades, the major function of mRNA was thought to be to provide protein-coding information embedded in the genome. The advent of high-throughput sequencing has led to the discovery of pervasive transcription of eukaryotic genomes and opened the world of RNA-mediated gene regulation. Many regulatory RNAs have been found to be incapable of protein coding and are hence termed as non-coding RNAs (ncRNAs). However, studies in recent years have shown that several previously annotated non-coding RNAs have the potential to encode proteins, and conversely, some coding RNAs have regulatory functions independent of the protein they encode. Such bi-functional RNAs, with both protein coding and non-coding functions, which we term as ‘cncRNAs’, have emerged as new players in cellular systems. Here, we describe the functions of some cncRNAs identified from bacteria to humans. Because the functions of many RNAs across genomes remains unclear, we propose that RNAs be classified as coding, non-coding or both only after careful analysis of their functions. PMID:26498036

Computerized bar code-based blood identification systems and near-miss transfusion episodes and transfusion errors.

PubMed

Nuttall, Gregory A; Abenstein, John P; Stubbs, James R; Santrach, Paula; Ereth, Mark H; Johnson, Pamela M; Douglas, Emily; Oliver, William C

2013-04-01

To determine whether the use of a computerized bar code-based blood identification system resulted in a reduction in transfusion errors or near-miss transfusion episodes. Our institution instituted a computerized bar code-based blood identification system in October 2006. After institutional review board approval, we performed a retrospective study of transfusion errors from January 1, 2002, through December 31, 2005, and from January 1, 2007, through December 31, 2010. A total of 388,837 U were transfused during the 2002-2005 period. There were 6 misidentification episodes of a blood product being transfused to the wrong patient during that period (incidence of 1 in 64,806 U or 1.5 per 100,000 transfusions; 95% CI, 0.6-3.3 per 100,000 transfusions). There was 1 reported near-miss transfusion episode (incidence of 0.3 per 100,000 transfusions; 95% CI, <0.1-1.4 per 100,000 transfusions). A total of 304,136 U were transfused during the 2007-2010 period. There was 1 misidentification episode of a blood product transfused to the wrong patient during that period when the blood bag and patient's armband were scanned after starting to transfuse the unit (incidence of 1 in 304,136 U or 0.3 per 100,000 transfusions; 95% CI, <0.1-1.8 per 100,000 transfusions; P=.14). There were 34 reported near-miss transfusion errors (incidence of 11.2 per 100,000 transfusions; 95% CI, 7.7-15.6 per 100,000 transfusions; P<.001). Institution of a computerized bar code-based blood identification system was associated with a large increase in discovered near-miss events. Copyright © 2013 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Identification of coding and non-coding mutational hotspots in cancer genomes.

PubMed

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

Evaluation of non-coding variation in GLUT1 deficiency.

PubMed

Liu, Yu-Chi; Lee, Jia Wei Audrey; Bellows, Susannah T; Damiano, John A; Mullen, Saul A; Berkovic, Samuel F; Bahlo, Melanie; Scheffer, Ingrid E; Hildebrand, Michael S

2016-12-01

Loss-of-function mutations in SLC2A1, encoding glucose transporter-1 (GLUT-1), lead to dysfunction of glucose transport across the blood-brain barrier. Ten percent of cases with hypoglycorrhachia (fasting cerebrospinal fluid [CSF] glucose <2.2mmol/L) do not have mutations. We hypothesized that GLUT1 deficiency could be due to non-coding SLC2A1 variants. We performed whole exome sequencing of one proband with a GLUT1 phenotype and hypoglycorrhachia negative for SLC2A1 sequencing and copy number variants. We studied a further 55 patients with different epilepsies and low CSF glucose who did not have exonic mutations or copy number variants. We sequenced non-coding promoter and intronic regions. We performed mRNA studies for the recurrent intronic variant. The proband had a de novo splice site mutation five base pairs from the intron-exon boundary. Three of 55 patients had deep intronic SLC2A1 variants, including a recurrent variant in two. The recurrent variant produced less SLC2A1 mRNA transcript. Fasting CSF glucose levels show an age-dependent correlation, which makes the definition of hypoglycorrhachia challenging. Low CSF glucose levels may be associated with pathogenic SLC2A1 mutations including deep intronic SLC2A1 variants. Extending genetic screening to non-coding regions will enable diagnosis of more patients with GLUT1 deficiency, allowing implementation of the ketogenic diet to improve outcomes. © 2016 Mac Keith Press.

21 CFR 610.67 - Bar code label requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... or to blood and blood components intended for transfusion. For blood and blood components intended...) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.67 Bar code label requirements. Biological products must comply with the bar code requirements at § 201.25 of this chapter. However, the bar...

21 CFR 610.67 - Bar code label requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... or to blood and blood components intended for transfusion. For blood and blood components intended...) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.67 Bar code label requirements. Biological products must comply with the bar code requirements at § 201.25 of this chapter. However, the bar...

21 CFR 610.67 - Bar code label requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... or to blood and blood components intended for transfusion. For blood and blood components intended...) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.67 Bar code label requirements. Biological products must comply with the bar code requirements at § 201.25 of this chapter. However, the bar...

Non-coding glucometers among pediatric patients with diabetes: looking for the target population and an accuracy evaluation of no-coding personal glucometer.

PubMed

Fendler, Wojciech; Hogendorf, Anna; Szadkowska, Agnieszka; Młynarski, Wojciech

2011-01-01

Self-monitoring of blood glucose (SMBG) is one of the cornerstones of diabetes management. To evaluate the potential for miscoding of a personal glucometer, to define a target population among pediatric patients with diabetes for a non-coding glucometer and the accuracy of the Contour TS non-coding system. Potential for miscoding during self-monitoring of blood glucose was evaluated by means of an anonymous questionnaire, with worst and best case scenarios evaluated depending on the responses pattern. Testing of the Contour TS system was performed according to guidelines set by the national committee for clinical laboratory standards. Estimated frequency of individuals prone to non-coding ranged from 68.21% (95% 60.70- 75.72%) to 7.95% (95%CI 3.86-12.31%) for the worse and best case scenarios respectively. Factors associated with increased likelihood of non-coding were: a smaller number of tests per day, a greater number of individuals involved in testing and self-testing by the patient with diabetes. The Contour TS device showed intra- and inter-assay accuracy -95%, linear association with laboratory measurements (R2=0.99, p <0.0001) and consistent, but small bias of -1.12% (95% Confidence Interval -3.27 to 1.02%). Clarke error grid analysis showed 4% of values within the benign error zone (B) with the other measurements yielding an acceptably accurate result (zone A). The Contour TS system showed sufficient accuracy to be safely used in monitoring of pediatric diabetic patients. Patients from families with a high throughput of test-strips or multiple individuals involved in SMBG using the same meter are candidates for clinical use of such devices due to an increased risk of calibration errors.

Role of non-coding RNAs in non-aging-related neurological disorders.

PubMed

Vieira, A S; Dogini, D B; Lopes-Cendes, I

2018-06-11

Protein coding sequences represent only 2% of the human genome. Recent advances have demonstrated that a significant portion of the genome is actively transcribed as non-coding RNA molecules. These non-coding RNAs are emerging as key players in the regulation of biological processes, and act as "fine-tuners" of gene expression. Neurological disorders are caused by a wide range of genetic mutations, epigenetic and environmental factors, and the exact pathophysiology of many of these conditions is still unknown. It is currently recognized that dysregulations in the expression of non-coding RNAs are present in many neurological disorders and may be relevant in the mechanisms leading to disease. In addition, circulating non-coding RNAs are emerging as potential biomarkers with great potential impact in clinical practice. In this review, we discuss mainly the role of microRNAs and long non-coding RNAs in several neurological disorders, such as epilepsy, Huntington disease, fragile X-associated ataxia, spinocerebellar ataxias, amyotrophic lateral sclerosis (ALS), and pain. In addition, we give information about the conditions where microRNAs have demonstrated to be potential biomarkers such as in epilepsy, pain, and ALS.

FDA’s Nozzle Numerical Simulation Challenge: Non-Newtonian Fluid Effects and Blood Damage

PubMed Central

Trias, Miquel; Arbona, Antonio; Massó, Joan; Miñano, Borja; Bona, Carles

2014-01-01

Data from FDA’s nozzle challenge–a study to assess the suitability of simulating fluid flow in an idealized medical device–is used to validate the simulations obtained from a numerical, finite-differences code. Various physiological indicators are computed and compared with experimental data from three different laboratories, getting a very good agreement. Special care is taken with the derivation of blood damage (hemolysis). The paper is focused on the laminar regime, in order to investigate non-Newtonian effects (non-constant fluid viscosity). The code can deal with these effects with just a small extra computational cost, improving Newtonian estimations up to a ten percent. The relevance of non-Newtonian effects for hemolysis parameters is discussed. PMID:24667931

Differential expression and emerging functions of non-coding RNAs in cold adaptation.

PubMed

Frigault, Jacques J; Morin, Mathieu D; Morin, Pier Jr

2017-01-01

Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.

Non-coding RNAs in lung cancer

PubMed Central

Ricciuti, Biagio; Mecca, Carmen; Crinò, Lucio; Baglivo, Sara; Cenci, Matteo; Metro, Giulio

2014-01-01

The discovery that protein-coding genes represent less than 2% of all human genome, and the evidence that more than 90% of it is actively transcribed, changed the classical point of view of the central dogma of molecular biology, which was always based on the assumption that RNA functions mainly as an intermediate bridge between DNA sequences and protein synthesis machinery. Accumulating data indicates that non-coding RNAs are involved in different physiological processes, providing for the maintenance of cellular homeostasis. They are important regulators of gene expression, cellular differentiation, proliferation, migration, apoptosis, and stem cell maintenance. Alterations and disruptions of their expression or activity have increasingly been associated with pathological changes of cancer cells, this evidence and the prospect of using these molecules as diagnostic markers and therapeutic targets, make currently non-coding RNAs among the most relevant molecules in cancer research. In this paper we will provide an overview of non-coding RNA function and disruption in lung cancer biology, also focusing on their potential as diagnostic, prognostic and predictive biomarkers. PMID:25593996

[Medical and economic evaluation of donated blood screening for hepatitis C and non-A, non-B, non-C hepatitis].

PubMed

Vergnon, P; Colin, C; Jullien, A M; Bory, E; Excoffier, S; Matillon, Y; Trepo, C

1996-01-01

The aim of this study was to evaluate the cost of hepatitis C and non-A non-B non-C screening strategy in donated blood, currently used in French transfusion centres and to assess the effect in the blood transfusion centres according to the prevalence of the disease and the intrinsec values of tests. This screening strategy was based on alanine aminotransferase assay, and HBc and HCV antibodies detection. In 1993, a survey was conducted in 26 French transfusion centers to estimate the costs of the screening strategy currently used. Average expenditure on diagnostic sets, equipment, staff and administration charges for hepatitis C and non-A non-B non-C screening were calculated. From these results, we estimated the cost of the previous strategy which did not involve HCV antibody testing, so as to determine the incremental cost between the two strategies. We used clinical decision analysis and sensitivity analysis to estimate the incremental cost-effectiveness ratio with data gathered from the literature and examine the impact on blood transfusion centre. Implemented for 100,000 volunteer blood donations, the incremental cost of the new strategy was FF 2,566,111 (1992) and the marginal effectiveness was 180 additional infected donations detected. The sensitivity analysis showed the major influence of infection prevalence in donated blood on the incremental cost-effectiveness ratio: the lower the prevalence, the higher the cost-effectiveness ratio per contaminated blood product avoided.

21 CFR 607.40 - Establishment registration and blood product listing requirements for foreign blood product...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Establishment registration and blood product listing requirements for foreign blood product establishments. 607.40 Section 607.40 Food and Drugs FOOD... REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Foreign...

21 CFR 607.40 - Establishment registration and blood product listing requirements for foreign blood product...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Establishment registration and blood product listing requirements for foreign blood product establishments. 607.40 Section 607.40 Food and Drugs FOOD... REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Foreign...

21 CFR 607.40 - Establishment registration and blood product listing requirements for foreign blood product...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Establishment registration and blood product listing requirements for foreign blood product establishments. 607.40 Section 607.40 Food and Drugs FOOD... REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Foreign...

21 CFR 607.40 - Establishment registration and blood product listing requirements for foreign blood product...

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Establishment registration and blood product listing requirements for foreign blood product establishments. 607.40 Section 607.40 Food and Drugs FOOD... REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Foreign...

21 CFR 607.40 - Establishment registration and blood product listing requirements for foreign blood product...

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Establishment registration and blood product listing requirements for foreign blood product establishments. 607.40 Section 607.40 Food and Drugs FOOD... REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Foreign...

Live Donor Liver Transplantation Without Blood Products

PubMed Central

Jabbour, Nicolas; Gagandeep, Singh; Mateo, Rodrigo; Sher, Linda; Strum, Earl; Donovan, John; Kahn, Jeffrey; Peyre, Christian G.; Henderson, Randy; Fong, Tse-Ling; Selby, Rick; Genyk, Yuri

2004-01-01

Objective: Developing strategies for transfusion-free live donor liver transplantation in Jehovah's Witness patients. Summary Background Data: Liver transplantation is the standard of care for patients with end-stage liver disease. A disproportionate increase in transplant candidates and an allocation policy restructuring, favoring patients with advanced disease, have led to longer waiting time and increased medical acuity for transplant recipients. Consequently, Jehovah's Witness patients, who refuse blood product transfusion, are usually excluded from liver transplantation. We combined blood augmentation and conservation practices with live donor liver transplantation (LDLT) to accomplish successful LDLT in Jehovah's Witness patients without blood products. Our algorithm provides broad possibilities for blood conservation for all surgical patients. Methods: From September 1998 until June 2001, 38 LDLTs were performed at Keck USC School of Medicine: 8 in Jehovah's Witness patients (transfusion-free group) and 30 in non-Jehovah's Witness patients (transfusion-eligible group). All transfusion-free patients underwent preoperative blood augmentation with erythropoietin, intraoperative cell salvage, and acute normovolemic hemodilution. These techniques were used in only 7%, 80%, and 10%, respectively, in transfusion-eligible patients. Perioperative clinical data and outcomes were retrospectively reviewed. Data from both groups were statistically analyzed. Results: Preoperative liver disease severity was similar in both groups; however, transfusion-free patients had significantly higher hematocrit levels following erythropoietin augmentation. Operative time, blood loss, and postoperative hematocrits were similar in both groups. No blood products were used in transfusion-free patients while 80% of transfusion-eligible patients received a median of 4.5+/− 3.5 units of packed red cell. ICU and total hospital stay were similar in both groups. The survival rate was 100% in

Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection

USDA-ARS?s Scientific Manuscript database

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

[Relevance of long non-coding RNAs in tumour biology].

PubMed

Nagy, Zoltán; Szabó, Diána Rita; Zsippai, Adrienn; Falus, András; Rácz, Károly; Igaz, Péter

2012-09-23

The discovery of the biological relevance of non-coding RNA molecules represents one of the most significant advances in contemporary molecular biology. It has turned out that a major fraction of the non-coding part of the genome is transcribed. Beside small RNAs (including microRNAs) more and more data are disclosed concerning long non-coding RNAs of 200 nucleotides to 100 kb length that are implicated in the regulation of several basic molecular processes (cell proliferation, chromatin functioning, microRNA-mediated effects, etc.). Some of these long non-coding RNAs have been associated with human tumours, including H19, HOTAIR, MALAT1, etc., the different expression of which has been noted in various neoplasms relative to healthy tissues. Long non-coding RNAs may represent novel markers of molecular diagnostics and they might even turn out to be targets of therapeutic intervention.

Metformin-Induced Changes of the Coding Transcriptome and Non-Coding RNAs in the Livers of Non-Alcoholic Fatty Liver Disease Mice.

PubMed

Guo, Jun; Zhou, Yuan; Cheng, Yafen; Fang, Weiwei; Hu, Gang; Wei, Jie; Lin, Yajun; Man, Yong; Guo, Lixin; Sun, Mingxiao; Cui, Qinghua; Li, Jian

2018-01-01

Recent studies have suggested that changes in non-coding mRNA play a key role in the progression of non-alcoholic fatty liver disease (NAFLD). Metformin is now recommended and effective for the treatment of NAFLD. We hope the current analyses of the non-coding mRNA transcriptome will provide a better presentation of the potential roles of mRNAs and long non-coding RNAs (lncRNAs) that underlie NAFLD and metformin intervention. The present study mainly analysed changes in the coding transcriptome and non-coding RNAs after the application of a five-week metformin intervention. Liver samples from three groups of mice were harvested for transcriptome profiling, which covered mRNA, lncRNA, microRNA (miRNA) and circular RNA (circRNA), using a microarray technique. A systematic alleviation of high-fat diet (HFD)-induced transcriptome alterations by metformin was observed. The metformin treatment largely reversed the correlations with diabetes-related pathways. Our analysis also suggested interaction networks between differentially expressed lncRNAs and known hepatic disease genes and interactions between circRNA and their disease-related miRNA partners. Eight HFD-responsive lncRNAs and three metformin-responsive lncRNAs were noted due to their widespread associations with disease genes. Moreover, seven miRNAs that interacted with multiple differentially expressed circRNAs were highlighted because they were likely to be associated with metabolic or liver diseases. The present study identified novel changes in the coding transcriptome and non-coding RNAs in the livers of NAFLD mice after metformin treatment that might shed light on the underlying mechanism by which metformin impedes the progression of NAFLD. © 2018 The Author(s). Published by S. Karger AG, Basel.

Non-coding functions of alternative pre-mRNA splicing in development

PubMed Central

Mockenhaupt, Stefan; Makeyev, Eugene V.

2015-01-01

A majority of messenger RNA precursors (pre-mRNAs) in the higher eukaryotes undergo alternative splicing to generate more than one mature product. By targeting the open reading frame region this process increases diversity of protein isoforms beyond the nominal coding capacity of the genome. However, alternative splicing also frequently controls output levels and spatiotemporal features of cellular and organismal gene expression programs. Here we discuss how these non-coding functions of alternative splicing contribute to development through regulation of mRNA stability, translational efficiency and cellular localization. PMID:26493705

21 CFR 207.7 - Establishment registration and product listing for human blood and blood products and for medical...

Code of Federal Regulations, 2012 CFR

2012-04-01

... human blood and blood products and for medical devices. 207.7 Section 207.7 Food and Drugs FOOD AND DRUG... product listing for human blood and blood products and for medical devices. (a) Owners and operators of human blood and blood product establishments shall register and list their products with the Center for...

21 CFR 207.7 - Establishment registration and product listing for human blood and blood products and for medical...

Code of Federal Regulations, 2014 CFR

2014-04-01

... human blood and blood products and for medical devices. 207.7 Section 207.7 Food and Drugs FOOD AND DRUG... product listing for human blood and blood products and for medical devices. (a) Owners and operators of human blood and blood product establishments shall register and list their products with the Center for...

21 CFR 207.7 - Establishment registration and product listing for human blood and blood products and for medical...

Code of Federal Regulations, 2013 CFR

2013-04-01

... human blood and blood products and for medical devices. 207.7 Section 207.7 Food and Drugs FOOD AND DRUG... product listing for human blood and blood products and for medical devices. (a) Owners and operators of human blood and blood product establishments shall register and list their products with the Center for...

Blood product transfusions and reactions.

PubMed

Osterman, Jessica L; Arora, Sanjay

2014-08-01

Blood product transfusions are an essential component of the practice of emergency medicine. From acute traumatic hemorrhage to chronic blood loss necessitating transfusion for symptomatic anemia, familiarity with individual blood products and their indications for transfusion is an essential tool for every emergency physician (EP). Although the focus of this article is primarily on the transfusion of red blood cells, many of the concepts are applicable to the transfusion of all blood products. EPs must be fully familiar with both the individual blood components and the potential reactions and complications of these transfusions. Copyright © 2014 Elsevier Inc. All rights reserved.

Blood Product Transfusions and Reactions.

PubMed

Osterman, Jessica L; Arora, Sanjay

2017-12-01

Blood product transfusions are an essential component of the practice of emergency medicine. From acute traumatic hemorrhage to chronic blood loss necessitating transfusion for symptomatic anemia, familiarity with individual blood products and their indications for transfusion is an essential tool for every emergency physician (EP). Although the focus of this article is primarily on the transfusion of red blood cells, many of the concepts are applicable to the transfusion of all blood products. EPs must be fully familiar with both the individual blood components and the potential reactions and complications of these transfusions. Copyright © 2017 Elsevier Inc. All rights reserved.

Economic burden of non-malignant blood disorders across Europe: a population-based cost study.

PubMed

Luengo-Fernandez, Ramon; Burns, Richeal; Leal, Jose

2016-08-01

Blood disorders comprise a wide range of diseases including anaemia, malignant blood disorders, and haemorrhagic disorders. Although they are a common cause of disease, no systematic cost-of-illness studies have been done to assess the economic effect of non-malignant blood disorders in Europe. We aimed to assess the economic burden of non-malignant blood disorders across the 28 countries of the European Union (EU), Iceland, Norway, and Switzerland. Non-malignant blood disorder-related costs (WHO International Classification of Diseases, 10th revision [ICD] D50-89) were estimated for 28 EU countries, Iceland, Norway, and Switzerland for 2012. Country-specific costs were estimated with aggregate data on morbidity, mortality, and health-care resource use obtained from international and national sources. Health-care costs were estimated from expenditure on primary care, outpatient care, emergency care, hospital inpatient care, and drugs. Costs of informal care and productivity losses due to morbidity and early death were also included. To these costs we added those due to malignant blood disorders (ICD-10 C81-96 and D47) as estimated in a Burns and colleagues' companion Article to obtain the total costs of blood disorders. Non-malignant disorders of the blood cost the 31 European countries €11 billion in 2012. Health-care costs accounted for €8 billion (75% of total costs), productivity losses for €2 billion (19%), and informal care for less than €1 billion (6%). Averaged across the European population studied, non-malignant disorders of the blood represented an annual health-care cost of €159 per ten citizens. Combining malignant and non-malignant blood disorders, the total cost of blood disorders was €23 billion in 2012. Our study highlights the economic burden that non-malignant blood disorders place on European health-care systems and societies. Our study also shows that blood disorder costs were evenly distributed between malignant and non

Non-coding RNA networks in cancer.

PubMed

Anastasiadou, Eleni; Jacob, Leni S; Slack, Frank J

2018-01-01

Thousands of unique non-coding RNA (ncRNA) sequences exist within cells. Work from the past decade has altered our perception of ncRNAs from 'junk' transcriptional products to functional regulatory molecules that mediate cellular processes including chromatin remodelling, transcription, post-transcriptional modifications and signal transduction. The networks in which ncRNAs engage can influence numerous molecular targets to drive specific cell biological responses and fates. Consequently, ncRNAs act as key regulators of physiological programmes in developmental and disease contexts. Particularly relevant in cancer, ncRNAs have been identified as oncogenic drivers and tumour suppressors in every major cancer type. Thus, a deeper understanding of the complex networks of interactions that ncRNAs coordinate would provide a unique opportunity to design better therapeutic interventions.

Non-coding functions of alternative pre-mRNA splicing in development.

PubMed

Mockenhaupt, Stefan; Makeyev, Eugene V

2015-12-01

A majority of messenger RNA precursors (pre-mRNAs) in the higher eukaryotes undergo alternative splicing to generate more than one mature product. By targeting the open reading frame region this process increases diversity of protein isoforms beyond the nominal coding capacity of the genome. However, alternative splicing also frequently controls output levels and spatiotemporal features of cellular and organismal gene expression programs. Here we discuss how these non-coding functions of alternative splicing contribute to development through regulation of mRNA stability, translational efficiency and cellular localization. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Long Non-Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed-Batch Conditions.

PubMed

Vito, Davide; Smales, C Mark

2018-05-21

The role of non-coding RNAs in determining growth, productivity and recombinant product quality attributes in Chinese hamster ovary (CHO) cells has received much attention in recent years, exemplified by studies into microRNAs in particular. However, other classes of non-coding RNAs have received less attention. One such class are the non-coding RNAs known collectively as long non-coding RNAs (lncRNAs). We have undertaken the first landscape analysis of the lncRNA transcriptome in CHO using a mouse based microarray that also provided for the surveillance of the coding transcriptome. We report on those lncRNAs present in a model host CHO cell line under batch and fed-batch conditions on two different days and relate the expression of different lncRNAs to each other. We demonstrate that the mouse microarray was suitable for the detection and analysis of thousands of CHO lncRNAs and validated a number of these by qRT-PCR. We then further analysed the data to identify those lncRNAs whose expression changed the most between growth and stationary phases of culture or between batch and fed-batch culture to identify potential lncRNA targets for further functional studies with regard to their role in controlling growth of CHO cells. We discuss the implications for the publication of this rich dataset and how this may be used by the community. This article is protected by copyright. All rights reserved.

Facts and updates about cardiovascular non-coding RNAs in heart failure.

PubMed

Thum, Thomas

2015-09-01

About 11% of all deaths include heart failure as a contributing cause. The annual cost of heart failure amounts to US $34,000,000,000 in the United States alone. With the exception of heart transplantation, there is no curative therapy available. Only occasionally there are new areas in science that develop into completely new research fields. The topic on non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, is such a field. In this short review, we will discuss the latest developments about non-coding RNAs in cardiovascular disease. MicroRNAs are short regulatory non-coding endogenous RNA species that are involved in virtually all cellular processes. Long non-coding RNAs also regulate gene and protein levels; however, by much more complicated and diverse mechanisms. In general, non-coding RNAs have been shown to be of great value as therapeutic targets in adverse cardiac remodelling and also as diagnostic and prognostic biomarkers for heart failure. In the future, non-coding RNA-based therapeutics are likely to enter the clinical reality offering a new treatment approach of heart failure.

Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

PubMed

Tani, Hidenori

2017-03-22

Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 < 4 h) include known regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

Regulation of mammalian cell differentiation by long non-coding RNAs

PubMed Central

Hu, Wenqian; Alvarez-Dominguez, Juan R; Lodish, Harvey F

2012-01-01

Differentiation of specialized cell types from stem and progenitor cells is tightly regulated at several levels, both during development and during somatic tissue homeostasis. Many long non-coding RNAs have been recognized as an additional layer of regulation in the specification of cellular identities; these non-coding species can modulate gene-expression programmes in various biological contexts through diverse mechanisms at the transcriptional, translational or messenger RNA stability levels. Here, we summarize findings that implicate long non-coding RNAs in the control of mammalian cell differentiation. We focus on several representative differentiation systems and discuss how specific long non-coding RNAs contribute to the regulation of mammalian development. PMID:23070366

The development of non-coding RNA ontology.

PubMed

Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A; Dou, Dejing; Huang, Weili; Natale, Darren A; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T; Jiang, Guoqian; Lin, Yu; Wu, Bin; Strachan, Harrison J; de Silva, Nisansa; Kasukurthi, Mohan Vamsi; Jha, Vikash Kumar; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming

2016-01-01

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

DNA rearrangements directed by non-coding RNAs in ciliates

PubMed Central

Mochizuki, Kazufumi

2013-01-01

Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA descrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non-coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non-coding RNAs that are produced and utilized in an RNAi-related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole-genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA descrambling in Oxytricha is guided by long non-coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct descrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non-coding RNAs. PMID:21956937

Long Non-Coding RNAs Regulating Immunity in Insects

PubMed Central

Satyavathi, Valluri; Ghosh, Rupam; Subramanian, Srividya

2017-01-01

Recent advances in modern technology have led to the understanding that not all genetic information is coded into protein and that the genomes of each and every organism including insects produce non-coding RNAs that can control different biological processes. Among RNAs identified in the last decade, long non-coding RNAs (lncRNAs) represent a repertoire of a hidden layer of internal signals that can regulate gene expression in physiological, pathological, and immunological processes. Evidence shows the importance of lncRNAs in the regulation of host–pathogen interactions. In this review, an attempt has been made to view the role of lncRNAs regulating immune responses in insects. PMID:29657286

Biological significance of long non-coding RNA FTX expression in human colorectal cancer

PubMed Central

Guo, Xiao-Bo; Hua, Zhu; Li, Chen; Peng, Li-Pan; Wang, Jing-Shen; Wang, Bo; Zhi, Qiao-Ming

2015-01-01

The purpose of this study was to determine the expression of long non-coding RNA (lncRNA) FTX and analyze its prognostic and biological significance in colorectal cancer (CRC). A quantitative reverse transcription PCR was performed to detect the expression of long non-coding RNA FTX in 35 pairs of colorectal cancer and corresponding noncancerous tissues. The expression of long non-coding RNA FTX was detected in 187 colorectal cancer tissues and its correlations with clinicopathological factors of patients were examined. Univariate and multivariate analyses were performed to analyze the prognostic significance of Long Non-coding RNA FTX expression. The effects of long non-coding RNA FTX expression on malignant phenotypes of colorectal cancer cells and its possible biological significances were further determined. Long non-coding RNA FTX was significantly upregulated in colorectal cancer tissues, and low long non-coding RNA FTX expression was significantly correlated with differentiation grade, lymph vascular invasion, and clinical stage. Patients with high long non-coding RNA FTX showed poorer overall survival than those with low long non-coding RNA FTX. Multivariate analyses indicated that status of long non-coding RNA FTX was an independent prognostic factor for patients. Functional analyses showed that upregulation of long non-coding RNA FTX significantly promoted growth, migration, invasion, and increased colony formation in colorectal cancer cells. Therefore, long non-coding RNA FTX may be a potential biomarker for predicting the survival of colorectal cancer patients and might be a molecular target for treatment of human colorectal cancer. PMID:26629053

Biological significance of long non-coding RNA FTX expression in human colorectal cancer.

PubMed

Guo, Xiao-Bo; Hua, Zhu; Li, Chen; Peng, Li-Pan; Wang, Jing-Shen; Wang, Bo; Zhi, Qiao-Ming

2015-01-01

The purpose of this study was to determine the expression of long non-coding RNA (lncRNA) FTX and analyze its prognostic and biological significance in colorectal cancer (CRC). A quantitative reverse transcription PCR was performed to detect the expression of long non-coding RNA FTX in 35 pairs of colorectal cancer and corresponding noncancerous tissues. The expression of long non-coding RNA FTX was detected in 187 colorectal cancer tissues and its correlations with clinicopathological factors of patients were examined. Univariate and multivariate analyses were performed to analyze the prognostic significance of Long Non-coding RNA FTX expression. The effects of long non-coding RNA FTX expression on malignant phenotypes of colorectal cancer cells and its possible biological significances were further determined. Long non-coding RNA FTX was significantly upregulated in colorectal cancer tissues, and low long non-coding RNA FTX expression was significantly correlated with differentiation grade, lymph vascular invasion, and clinical stage. Patients with high long non-coding RNA FTX showed poorer overall survival than those with low long non-coding RNA FTX. Multivariate analyses indicated that status of long non-coding RNA FTX was an independent prognostic factor for patients. Functional analyses showed that upregulation of long non-coding RNA FTX significantly promoted growth, migration, invasion, and increased colony formation in colorectal cancer cells. Therefore, long non-coding RNA FTX may be a potential biomarker for predicting the survival of colorectal cancer patients and might be a molecular target for treatment of human colorectal cancer.

Production code control system for hydrodynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slone, D.M.

1997-08-18

We describe how the Production Code Control System (pCCS), written in Perl, has been used to control and monitor the execution of a large hydrodynamics simulation code in a production environment. We have been able to integrate new, disparate, and often independent, applications into the PCCS framework without the need to modify any of our existing application codes. Both users and code developers see a consistent interface to the simulation code and associated applications regardless of the physical platform, whether an MPP, SMP, server, or desktop workstation. We will also describe our use of Perl to develop a configuration managementmore » system for the simulation code, as well as a code usage database and report generator. We used Perl to write a backplane that allows us plug in preprocessors, the hydrocode, postprocessors, visualization tools, persistent storage requests, and other codes. We need only teach PCCS a minimal amount about any new tool or code to essentially plug it in and make it usable to the hydrocode. PCCS has made it easier to link together disparate codes, since using Perl has removed the need to learn the idiosyncrasies of system or RPC programming. The text handling in Perl makes it easy to teach PCCS about new codes, or changes to existing codes.« less

Evolution of coding and non-coding genes in HOX clusters of a marsupial.

PubMed

Yu, Hongshi; Lindsay, James; Feng, Zhi-Ping; Frankenberg, Stephen; Hu, Yanqiu; Carone, Dawn; Shaw, Geoff; Pask, Andrew J; O'Neill, Rachel; Papenfuss, Anthony T; Renfree, Marilyn B

2012-06-18

The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

PubMed Central

2012-01-01

Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial. PMID:22708672

A cautionary tale: the non-causal association between type 2 diabetes risk SNP, rs7756992, and levels of non-coding RNA, CDKAL1-v1.

PubMed

Locke, Jonathan M; Wei, Fan-Yan; Tomizawa, Kazuhito; Weedon, Michael N; Harries, Lorna W

2015-04-01

Intronic single nucleotide polymorphisms (SNPs) in the CDKAL1 gene are associated with risk of developing type 2 diabetes. A strong correlation between risk alleles and lower levels of the non-coding RNA, CDKAL1-v1, has recently been reported in whole blood extracted from Japanese individuals. We sought to replicate this association in two independent cohorts: one using whole blood from white UK-resident individuals, and one using a collection of human pancreatic islets, a more relevant tissue type to study with respect to the aetiology of diabetes. Levels of CDKAL1-v1 were measured by real-time PCR using RNA extracted from human whole blood (n = 70) and human pancreatic islets (n = 48). Expression with respect to genotype was then determined. In a simple linear regression model, expression of CDKAL1-v1 was associated with the lead type 2 diabetes-associated SNP, rs7756992, in whole blood and islets. However, these associations were abolished or substantially reduced in multiple regression models taking into account rs9366357 genotype: a moderately linked SNP explaining a much larger amount of the variation in CDKAL1-v1 levels, but not strongly associated with risk of type 2 diabetes. Contrary to previous findings, we provide evidence against a role for dysregulated expression of CDKAL1-v1 in mediating the association between intronic SNPs in CDKAL1 and susceptibility to type 2 diabetes. The results of this study illustrate how caution should be exercised when inferring causality from an association between disease-risk genotype and non-coding RNA expression.

Integrating non-coding RNAs in JAK-STAT regulatory networks

PubMed Central

Witte, Steven; Muljo, Stefan A

2014-01-01

Being a well-characterized pathway, JAK-STAT signaling serves as a valuable paradigm for studying the architecture of gene regulatory networks. The discovery of untranslated or non-coding RNAs, namely microRNAs and long non-coding RNAs, provides an opportunity to elucidate their roles in such networks. In principle, these regulatory RNAs can act as downstream effectors of the JAK-STAT pathway and/or affect signaling by regulating the expression of JAK-STAT components. Examples of interactions between signaling pathways and non-coding RNAs have already emerged in basic cell biology and human diseases such as cancer, and can potentially guide the identification of novel biomarkers or drug targets for medicine. PMID:24778925

Lean coding machine. Facilities target productivity and job satisfaction with coding automation.

PubMed

Rollins, Genna

2010-07-01

Facilities are turning to coding automation to help manage the volume of electronic documentation, streamlining workflow, boosting productivity, and increasing job satisfaction. As EHR adoption increases, computer-assisted coding may become a necessity, not an option.

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus.

PubMed

Houtman, Miranda; Shchetynsky, Klementy; Chemin, Karine; Hensvold, Aase Haj; Ramsköld, Daniel; Tandre, Karolina; Eloranta, Maija-Leena; Rönnblom, Lars; Uebe, Steffen; Catrina, Anca Irinel; Malmström, Vivianne; Padyukov, Leonid

2018-06-01

Non-coding SNPs in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been linked with several autoimmune diseases, including rheumatoid arthritis, type I diabetes, and inflammatory bowel disease. However, the functional consequences of these SNPs are poorly characterized. Herein, we show in blood cells that SNPs in the PTPN2 locus are highly correlated with DNA methylation levels at four CpG sites downstream of PTPN2 and expression levels of the long non-coding RNA (lncRNA) LINC01882 downstream of these CpG sites. We observed that LINC01882 is mainly expressed in T cells and that anti-CD3/CD28 activated naïve CD4 + T cells downregulate the expression of LINC01882. RNA sequencing analysis of LINC01882 knockdown in Jurkat T cells, using a combination of antisense oligonucleotides and RNA interference, revealed the upregulation of the transcription factor ZEB1 and kinase MAP2K4, both involved in IL-2 regulation. Overall, our data suggests the involvement of LINC01882 in T cell activation and hints towards an auxiliary role of these non-coding SNPs in autoimmunity associated with the PTPN2 locus. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Low-dose exposure to bisphenols A, F and S of human primary adipocyte impacts coding and non-coding RNA profiles

PubMed Central

Leloire, Audrey; Dhennin, Véronique; Coumoul, Xavier; Yengo, Loïc; Froguel, Philippe

2017-01-01

Bisphenol A (BPA) exposure has been suspected to be associated with deleterious effects on health including obesity and metabolically-linked diseases. Although bisphenols F (BPF) and S (BPS) are BPA structural analogs commonly used in many marketed products as a replacement for BPA, only sparse toxicological data are available yet. Our objective was to comprehensively characterize bisphenols gene targets in a human primary adipocyte model, in order to determine whether they may induce cellular dysfunction, using chronic exposure at two concentrations: a “low-dose” similar to the dose usually encountered in human biological fluids and a higher dose. Therefore, BPA, BPF and BPS have been added at 10 nM or 10 μM during the differentiation of human primary adipocytes from subcutaneous fat of three non-diabetic Caucasian female patients. Gene expression (mRNA/lncRNA) arrays and microRNA arrays, have been used to assess coding and non-coding RNA changes. We detected significantly deregulated mRNA/lncRNA and miRNA at low and high doses. Enrichment in “cancer” and “organismal injury and abnormalities” related pathways was found in response to the three products. Some long intergenic non-coding RNAs and small nucleolar RNAs were differentially expressed suggesting that bisphenols may also activate multiple cellular processes and epigenetic modifications. The analysis of upstream regulators of deregulated genes highlighted hormones or hormone-like chemicals suggesting that BPS and BPF can be suspected to interfere, just like BPA, with hormonal regulation and have to be considered as endocrine disruptors. All these results suggest that as BPA, its substitutes BPS and BPF should be used with the same restrictions. PMID:28628672

Patient factors associated with non-attendance at colonoscopy after a positive screening faecal occult blood test.

PubMed

Plumb, Andrew A; Ghanouni, Alex; Rainbow, Sandra; Djedovic, Natasha; Marshall, Sarah; Stein, Judith; Taylor, Stuart A; Halligan, Steve; Lyratzopoulos, Georgios; von Wagner, Christian

2017-03-01

Background Screening participants with abnormal faecal occult blood test results who do not attend further testing are at high risk of colorectal cancer, yet little is known about their reasons for non-attendance. Methods We conducted a medical record review of 170 patients from two English Bowel Cancer Screening Programme centres who had abnormal guaiac faecal occult blood test screening tests between November 2011 and April 2013 but did not undergo colonoscopy. Using information from patient records, we coded and categorized reasons for non-attendance. Results Of the 170 patients, 82 were eligible for review, of whom 66 had at least one recorded reason for lack of colonoscopy follow-up. Reasons fell into seven main categories: (i) other commitments, (ii) unwillingness to have the test, (iii) a feeling that the faecal occult blood test result was a false positive, (iv) another health issue taking priority, (v) failing to complete bowel preparation, (vi) practical barriers (e.g. lack of transport), and (vii) having had or planning colonoscopy elsewhere. The most common single reasons were unwillingness to have a colonoscopy and being away. Conclusions We identify a range of apparent reasons for colonoscopy non-attendance after a positive faecal occult blood test screening. Education regarding the interpretation of guaiac faecal occult blood test findings, offer of alternative confirmatory test options, and flexibility in the timing or location of subsequent testing might decrease non-attendance of diagnostic testing following positive faecal occult blood test.

The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs.

PubMed

Shi, Lihua; Zhang, Zhe; Yu, Angela M; Wang, Wei; Wei, Zhi; Akhter, Ehtisham; Maurer, Kelly; Costa Reis, Patrícia; Song, Li; Petri, Michelle; Sullivan, Kathleen E

2014-01-01

Gene expression studies of peripheral blood mononuclear cells from patients with systemic lupus erythematosus (SLE) have demonstrated a type I interferon signature and increased expression of inflammatory cytokine genes. Studies of patients with Aicardi Goutières syndrome, commonly cited as a single gene model for SLE, have suggested that accumulation of non-coding RNAs may drive some of the pathologic gene expression, however, no RNA sequencing studies of SLE patients have been performed. This study was designed to define altered expression of coding and non-coding RNAs and to detect globally altered RNA processing in SLE. Purified monocytes from eight healthy age/gender matched controls and nine SLE patients (with low-moderate disease activity and lack of biologic drug use or immune suppressive treatment) were studied using RNA-seq. Quantitative RT-PCR was used to validate findings. Serum levels of endotoxin were measured by ELISA. We found that SLE patients had diminished expression of most endogenous retroviruses and small nucleolar RNAs, but exhibited increased expression of pri-miRNAs. Splicing patterns and polyadenylation were significantly altered. In addition, SLE monocytes expressed novel transcripts, an effect that was replicated by LPS treatment of control monocytes. We further identified increased circulating endotoxin in SLE patients. Monocytes from SLE patients exhibit globally dysregulated gene expression. The transcriptome is not simply altered by the transcriptional activation of a set of genes, but is qualitatively different in SLE. The identification of novel loci, inducible by LPS, suggests that chronic microbial translocation could contribute to the immunologic dysregulation in SLE, a new potential disease mechanism.

Quantitative analysis of optical properties of flowing blood using a photon-cell interactive Monte Carlo code: effects of red blood cells' orientation on light scattering.

PubMed

Sakota, Daisuke; Takatani, Setsuo

2012-05-01

Optical properties of flowing blood were analyzed using a photon-cell interactive Monte Carlo (pciMC) model with the physical properties of the flowing red blood cells (RBCs) such as cell size, shape, refractive index, distribution, and orientation as the parameters. The scattering of light by flowing blood at the He-Ne laser wavelength of 632.8 nm was significantly affected by the shear rate. The light was scattered more in the direction of flow as the flow rate increased. Therefore, the light intensity transmitted forward in the direction perpendicular to flow axis decreased. The pciMC model can duplicate the changes in the photon propagation due to moving RBCs with various orientations. The resulting RBC's orientation that best simulated the experimental results was with their long axis perpendicular to the direction of blood flow. Moreover, the scattering probability was dependent on the orientation of the RBCs. Finally, the pciMC code was used to predict the hematocrit of flowing blood with accuracy of approximately 1.0 HCT%. The photon-cell interactive Monte Carlo (pciMC) model can provide optical properties of flowing blood and will facilitate the development of the non-invasive monitoring of blood in extra corporeal circulatory systems.

Flavivirus RNAi suppression: decoding non-coding RNA.

PubMed

Pijlman, Gorben P

2014-08-01

Flaviviruses are important human pathogens that are transmitted by invertebrate vectors, mostly mosquitoes and ticks. During replication in their vector, flaviviruses are subject to a potent innate immune response known as antiviral RNA interference (RNAi). This defense mechanism is associated with the production of small interfering (si)RNA that lead to degradation of viral RNA. To what extent flaviviruses would benefit from counteracting antiviral RNAi is subject of debate. Here, the experimental evidence to suggest the existence of flavivirus RNAi suppressors is discussed. I will highlight the putative role of non-coding, subgenomic flavivirus RNA in suppression of RNAi in insect and mammalian cells. Novel insights from ongoing research will reveal how arthropod-borne viruses modulate innate immunity including antiviral RNAi. Copyright © 2014 Elsevier B.V. All rights reserved.

The Landscape of long non-coding RNA classification

PubMed Central

St Laurent, Georges; Wahlestedt, Claes; Kapranov, Philipp

2015-01-01

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long non-coding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the non-coding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual un-ambiguous classification framework results in a number of challenges in the annotation and interpretation of non-coding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets. PMID:25869999

Tracking blood products in blood centres using radio frequency identification: a comprehensive assessment.

PubMed

Davis, Rodeina; Geiger, Bradley; Gutierrez, Alfonso; Heaser, Julie; Veeramani, Dharmaraj

2009-07-01

Radio frequency identification (RFID) can be a key enabler for enhancing productivity and safety of the blood product supply chain. This article describes a systematic approach developed by the RFID Blood Consortium for a comprehensive feasibility and impact assessment of RFID application in blood centre operations. Our comprehensive assessment approach incorporates process-orientated and technological perspectives as well as impact analysis. Assessment of RFID-enabled process redesign is based on generic core processes derived from the three participating blood centres. The technological assessment includes RFID tag readability and performance evaluation, testing of temperature and biological effects of RF energy on blood products, and RFID system architecture design and standards. The scope of this article is limited to blood centre processes (from donation to manufacturing/distribution) for selected mainstream blood products (red blood cells and platelets). Radio frequency identification can help overcome a number of common challenges and process inefficiencies associated with identification and tracking of blood products. High frequency-based RFID technology performs adequately and safely for red blood cell and platelet products. Productivity and quality improvements in RFID-enabled blood centre processes can recoup investment cost in a 4-year payback period. Radio frequency identification application has significant process-orientated and technological implications. It is feasible and economically justifiable to incorporate RFID into blood centre processes.

In Vitro and Ex Vivo Approaches to Evaluate Next-Generation Tobacco and Non-Tobacco Products on Human Blood Platelets

PubMed Central

Spinelli, Sherry L.; Lannan, Katie L.; Loelius, Shannon G.

2017-01-01

Abstract Human blood platelets are major hemostatic regulators in the circulation and important in the mediation of chronic inflammation and immunomodulation. They are key elements that promote cardiovascular pathogenesis that leads to atherosclerosis, thrombosis, myocardial infarction, and stroke. New information on tobacco use and platelet dysregulation shows that these highly understudied vascular cells are dysregulated by tobacco smoke. Thus, platelet function studies should be an important consideration for the evaluation of existing and next-generation tobacco and non-tobacco products. Novel in vitro approaches are being sought to investigate these products and their influence on platelet function. Platelets are ideally suited for product assessment, as robust and novel in vitro translational methods are available to assess platelet function. Furthermore, the use of human biological systems has the advantage that risk predictions will better reflect the human condition. PMID:28337466

Functional interrogation of non-coding DNA through CRISPR genome editing.

PubMed

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Functional interrogation of non-coding DNA through CRISPR genome editing

PubMed Central

Canver, Matthew C.; Bauer, Daniel E.; Orkin, Stuart H.

2017-01-01

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. PMID:28288828

Behind the curtain of non-coding RNAs; long non-coding RNAs regulating hepatocarcinogenesis

PubMed Central

El Khodiry, Aya; Afify, Menna; El Tayebi, Hend M

2018-01-01

Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers worldwide. HCC is the fifth common malignancy in the world and the second leading cause of cancer death in Asia. Long non-coding RNAs (lncRNAs) are RNAs with a length greater than 200 nucleotides that do not encode proteins. lncRNAs can regulate gene expression and protein synthesis in several ways by interacting with DNA, RNA and proteins in a sequence specific manner. They could regulate cellular and developmental processes through either gene inhibition or gene activation. Many studies have shown that dysregulation of lncRNAs is related to many human diseases such as cardiovascular diseases, genetic disorders, neurological diseases, immune mediated disorders and cancers. However, the study of lncRNAs is challenging as they are poorly conserved between species, their expression levels aren’t as high as that of mRNAs and have great interpatient variations. The study of lncRNAs expression in cancers have been a breakthrough as it unveils potential biomarkers and drug targets for cancer therapy and helps understand the mechanism of pathogenesis. This review discusses many long non-coding RNAs and their contribution in HCC, their role in development, metastasis, and prognosis of HCC and how to regulate and target these lncRNAs as a therapeutic tool in HCC treatment in the future. PMID:29434445

The effects of blood and blood products on the arachnoid cell.

PubMed

Hansen, Eric A; Romanova, Liudmila; Janson, Christopher; Lam, Cornelius H

2017-06-01

After traumatic brain injury (TBI), large amounts of red blood cells and hemolytic products are deposited intracranially creating debris in the cerebrospinal fluid (CSF). This debris, which includes heme and bilirubin, is cleared via the arachnoid granulations and lymphatic systems. However, the mechanisms by which erythrocytes and their breakdown products interfere with normal CSF dynamics remain poorly defined. The purpose of this study was to model in vitro how blood breakdown products affect arachnoid cells at the CSF-blood barrier, and the extent to which the resorption of CSF into the venous drainage system is mechanically impaired following TBI. Arachnoid cells were grown to confluency on permeable membranes. Rates of growth and apoptosis were measured in the presence of blood and lysed blood, changes in transepithelial electrical resistance (TEER) was measured in the presence of blood and hemoglobin, and small molecule permeability was determined in the presence of blood, lysed blood, bilirubin, and biliverdin. These results were directly compared with an established rat brain endothelial cell line (RBEC4) co-cultured with rat brain astrocytes. We found that arachnoid cells grown in the presence of whole or lysed erythrocytes had significantly slower growth rates than controls. Bilirubin and biliverdin, despite their low solubilities, altered the paracellular transport of arachnoid cells more than the acute blood breakdown components of whole and lysed blood. Mannitol permeability was up to four times higher in biliverdin treatments than controls, and arachnoid membranes demonstrated significantly decreased small molecule permeabilities in the presence of whole and lysed blood. We conclude that short-term (<24 h) arachnoid cell transport and long-term (>5 days) arachnoid cell viability are affected by blood and blood breakdown products, with important consequences for CSF flow and blood clearance after TBI.

50 CFR Table 1c to Part 679 - Product Type Codes

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Product Type Codes 1c Table 1c to Part..., Table 1c Table 1c to Part 679—Product Type Codes Description Code Ancillary product.A product, such as... the highest recovery rate. P Reprocessed or rehandled product.A product, such as meal, that results...

21 CFR 607.30 - Updating blood product listing information.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Updating blood product listing information. 607.30... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.30 Updating blood product...

21 CFR 607.30 - Updating blood product listing information.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Updating blood product listing information. 607.30... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.30 Updating blood product...

21 CFR 607.30 - Updating blood product listing information.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Updating blood product listing information. 607.30... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.30 Updating blood product...

21 CFR 607.30 - Updating blood product listing information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Updating blood product listing information. 607.30... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.30 Updating blood product...

21 CFR 607.30 - Updating blood product listing information.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Updating blood product listing information. 607.30... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.30 Updating blood product...

Transfusion: -80°C Frozen Blood Products Are Safe and Effective in Military Casualty Care.

PubMed

Noorman, Femke; van Dongen, Thijs T C F; Plat, Marie-Christine J; Badloe, John F; Hess, John R; Hoencamp, Rigo

2016-01-01

The Netherlands Armed Forces use -80°C frozen red blood cells (RBCs), plasma and platelets combined with regular liquid stored RBCs, for the treatment of (military) casualties in Medical Treatment Facilities abroad. Our objective was to assess and compare the use of -80°C frozen blood products in combination with the different transfusion protocols and their effect on the outcome of trauma casualties. Hemovigilance and combat casualties data from Afghanistan 2006-2010 for 272 (military) trauma casualties with or without massive transfusions (MT: ≥6 RBC/24hr, N = 82 and non-MT: 1-5 RBC/24hr, N = 190) were analyzed retrospectively. In November 2007, a massive transfusion protocol (MTP; 4:3:1 RBC:Plasma:Platelets) for ATLS® class III/IV hemorrhage was introduced in military theatre. Blood product use, injury severity and mortality were assessed pre- and post-introduction of the MTP. Data were compared to civilian and military trauma studies to assess effectiveness of the frozen blood products and MTP. No ABO incompatible blood products were transfused and only 1 mild transfusion reaction was observed with 3,060 transfused products. In hospital mortality decreased post-MTP for MT patients from 44% to 14% (P = 0.005) and for non-MT patients from 12.7% to 5.9% (P = 0.139). Average 24-hour RBC, plasma and platelet ratios were comparable and accompanying 24-hour mortality rates were low compared to studies that used similar numbers of liquid stored (and on site donated) blood products. This report describes for the first time that the combination of -80°C frozen platelets, plasma and red cells is safe and at least as effective as standard blood products in the treatment of (military) trauma casualties. Frozen blood can save the lives of casualties of armed conflict without the need for in-theatre blood collection. These results may also contribute to solutions for logistic problems in civilian blood supply in remote areas.

Long non-coding RNAs in cancer metabolism.

PubMed

Xiao, Zhen-Dong; Zhuang, Li; Gan, Boyi

2016-10-01

Altered cellular metabolism is an emerging hallmark of cancer. Accumulating recent evidence links long non-coding RNAs (lncRNAs), a still poorly understood class of non-coding RNAs, to cancer metabolism. Here we review the emerging findings on the functions of lncRNAs in cancer metabolism, with particular emphasis on how lncRNAs regulate glucose and glutamine metabolism in cancer cells, discuss how lncRNAs regulate various aspects of cancer metabolism through their cross-talk with other macromolecules, explore the mechanistic conceptual framework of lncRNAs in reprogramming metabolism in cancers, and highlight the challenges in this field. A more in-depth understanding of lncRNAs in cancer metabolism may enable the development of novel and effective therapeutic strategies targeting cancer metabolism. © 2016 WILEY Periodicals, Inc.

Coherent state coding approaches the capacity of non-Gaussian bosonic channels

NASA Astrophysics Data System (ADS)

Huber, Stefan; König, Robert

2018-05-01

The additivity problem asks if the use of entanglement can boost the information-carrying capacity of a given channel beyond what is achievable by coding with simple product states only. This has recently been shown not to be the case for phase-insensitive one-mode Gaussian channels, but remains unresolved in general. Here we consider two general classes of bosonic noise channels, which include phase-insensitive Gaussian channels as special cases: these are attenuators with general, potentially non-Gaussian environment states and classical noise channels with general probabilistic noise. We show that additivity violations, if existent, are rather minor for all these channels: the maximal gain in classical capacity is bounded by a constant independent of the input energy. Our proof shows that coding by simple classical modulation of coherent states is close to optimal.

Long non-coding RNAs and their biological roles in plants.

PubMed

Liu, Xue; Hao, Lili; Li, Dayong; Zhu, Lihuang; Hu, Songnian

2015-06-01

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Non-coding variants contribute to the clinical heterogeneity of TTR amyloidosis.

PubMed

Iorio, Andrea; De Lillo, Antonella; De Angelis, Flavio; Di Girolamo, Marco; Luigetti, Marco; Sabatelli, Mario; Pradotto, Luca; Mauro, Alessandro; Mazzeo, Anna; Stancanelli, Claudia; Perfetto, Federico; Frusconi, Sabrina; My, Filomena; Manfellotto, Dario; Fuciarelli, Maria; Polimanti, Renato

2017-09-01

Coding mutations in TTR gene cause a rare hereditary form of systemic amyloidosis, which has a complex genotype-phenotype correlation. We investigated the role of non-coding variants in regulating TTR gene expression and consequently amyloidosis symptoms. We evaluated the genotype-phenotype correlation considering the clinical information of 129 Italian patients with TTR amyloidosis. Then, we conducted a re-sequencing of TTR gene to investigate how non-coding variants affect TTR expression and, consequently, phenotypic presentation in carriers of amyloidogenic mutations. Polygenic scores for genetically determined TTR expression were constructed using data from our re-sequencing analysis and the GTEx (Genotype-Tissue Expression) project. We confirmed a strong phenotypic heterogeneity across coding mutations causing TTR amyloidosis. Considering the effects of non-coding variants on TTR expression, we identified three patient clusters with specific expression patterns associated with certain phenotypic presentations, including late onset, autonomic neurological involvement, and gastrointestinal symptoms. This study provides novel data regarding the role of non-coding variation and the gene expression profiles in patients affected by TTR amyloidosis, also putting forth an approach that could be used to investigate the mechanisms at the basis of the genotype-phenotype correlation of the disease.

Decoding the function of nuclear long non-coding RNAs.

PubMed

Chen, Ling-Ling; Carmichael, Gordon G

2010-06-01

Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level. Copyright 2010 Elsevier Ltd. All rights reserved.

A-to-I editing of coding and non-coding RNAs by ADARs

PubMed Central

Nishikura, Kazuko

2016-01-01

Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. This A-to-I editing occurs not only in protein-coding regions of mRNAs, but also frequently in non-coding regions that contain inverted Alu repeats. Editing of coding sequences can result in the expression of functionally altered proteins that are not encoded in the genome, whereas the significance of Alu editing remains largely unknown. Certain microRNA (miRNA) precursors are also edited, leading to reduced expression or altered function of mature miRNAs. Conversely, recent studies indicate that ADAR1 forms a complex with Dicer to promote miRNA processing, revealing a new function of ADAR1 in the regulation of RNA interference. PMID:26648264

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

PubMed

Hezroni, Hadas; Ben-Tov Perry, Rotem; Meir, Zohar; Housman, Gali; Lubelsky, Yoav; Ulitsky, Igor

2017-08-30

Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.

Non-coding, mRNA-like RNAs database Y2K.

PubMed

Erdmann, V A; Szymanski, M; Hochberg, A; Groot, N; Barciszewski, J

2000-01-01

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www. man.poznan.pl/5SData/ncRNA/index.html

Unique identification code for medical fundus images using blood vessel pattern for tele-ophthalmology applications.

PubMed

Singh, Anushikha; Dutta, Malay Kishore; Sharma, Dilip Kumar

2016-10-01

Identification of fundus images during transmission and storage in database for tele-ophthalmology applications is an important issue in modern era. The proposed work presents a novel accurate method for generation of unique identification code for identification of fundus images for tele-ophthalmology applications and storage in databases. Unlike existing methods of steganography and watermarking, this method does not tamper the medical image as nothing is embedded in this approach and there is no loss of medical information. Strategic combination of unique blood vessel pattern and patient ID is considered for generation of unique identification code for the digital fundus images. Segmented blood vessel pattern near the optic disc is strategically combined with patient ID for generation of a unique identification code for the image. The proposed method of medical image identification is tested on the publically available DRIVE and MESSIDOR database of fundus image and results are encouraging. Experimental results indicate the uniqueness of identification code and lossless recovery of patient identity from unique identification code for integrity verification of fundus images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dysregulation of non-coding RNAs in gastric cancer

PubMed Central

Yang, Qing; Zhang, Ren-Wen; Sui, Peng-Cheng; He, Hai-Tao; Ding, Lei

2015-01-01

Gastric cancer (GC) is one of the most common cancers in the world and a significant threat to the health of patients, especially those from China and Japan. The prognosis for patients with late stage GC receiving the standard of care treatment, including surgery, chemotherapy and radiotherapy, remains poor. Developing novel treatment strategies, identifying new molecules for targeted therapy, and devising screening techniques to detect this cancer in its early stages are needed for GC patients. The discovery of non-coding RNAs (ncRNAs), primarily microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), helped to elucidate the mechanisms of tumorigenesis, diagnosis and treatment of GC. Recently, significant research has been conducted on non-coding RNAs and how the regulatory dysfunction of these RNAs impacts the tumorigenesis of GC. In this study, we review papers published in the last five years concerning the dysregulation of non-coding RNAs, especially miRNAs and lncRNAs, in GC. We summarize instances of aberrant expression of the ncRNAs in GC and their effect on survival-related events, including cell cycle regulation, AKT signaling, apoptosis and drug resistance. Additionally, we evaluate how ncRNA dysregulation affects the metastatic process, including the epithelial-mesenchymal transition, stem cells, transcription factor activity, and oncogene and tumor suppressor expression. Lastly, we determine how ncRNAs affect angiogenesis in the microenvironment of GC. We further discuss the use of ncRNAs as potential biomarkers for use in clinical screening, early diagnosis and prognosis of GC. At present, no ideal ncRNAs have been identified as targets for the treatment of GC. PMID:26494954

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

PubMed Central

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.

2012-01-01

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features. PMID:22362738

Effect of calcitriol on in vitro whole blood cytokine production in critically ill dogs.

PubMed

Jaffey, J A; Amorim, J; DeClue, A E

2018-06-01

Hypovitaminosis D has been identified as a predictor of mortality in human beings, dogs, cats and foals. However, the immunomodulatory effects of vitamin D in critically ill dogs has not been evaluated. The aim of this study was to evaluate the effect of calcitriol on cytokine production from whole blood collected from critically ill dogs in vitro. Twelve critically ill dogs admitted to a veterinary intensive care unit (ICU) were enrolled in a prospective cohort study. Whole blood from these dogs was incubated with calcitriol (2×10 -7 M) or ethanol (control) for 24h. Subsequent to this incubation, lipopolysaccharide (LPS)-stimulated whole blood production of tumor necrosis factor (TNF)-α, interleukin (IL)-6 and IL-10 were measured using a canine-specific multiplex assay. Calcitriol significantly increased LPS-stimulated whole blood production of IL-10 and decreased TNF-α production without significantly altering IL-6 production. There was no significant difference in whole blood cytokine production capacity between survivors and non-survivors at the time of discharge from the ICU or 30days after discharge. These data suggests that calcitriol induces an anti-inflammatory phenotype in vitro in whole blood from critically ill dogs. Copyright © 2018 Elsevier Ltd. All rights reserved.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

PubMed

Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

2012-01-01

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

ACON: a multipurpose production controller for plasma physics codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snell, C.

1983-01-01

ACON is a BCON controller designed to run large production codes on the CTSS Cray-1 or the LTSS 7600 computers. ACON can also be operated interactively, with input from the user's terminal. The controller can run one code or a sequence of up to ten codes during the same job. Options are available to get and save Mass storage files, to perform Historian file updating operations, to compile and load source files, and to send out print and film files. Special features include ability to retry after Mass failures, backup options for saving files, startup messages for the various codes,more » and ability to reserve specified amounts of computer time after successive code runs. ACON's flexibility and power make it useful for running a number of different production codes.« less

Master standard data quantity food production code. Macro elements for synthesizing production labor time.

PubMed

Matthews, M E; Waldvogel, C F; Mahaffey, M J; Zemel, P C

1978-06-01

Preparation procedures of standardized quantity formulas were analyzed for similarities and differences in production activities, and three entrée classifications were developed, based on these activities. Two formulas from each classification were selected, preparation procedures were divided into elements of production, and the MSD Quantity Food Production Code was applied. Macro elements not included in the existing Code were simulated, coded, assigned associated Time Measurement Units, and added to the MSD Quantity Food Production Code. Repeated occurrence of similar elements within production methods indicated that macro elements could be synthesized for use within one or more entrée classifications. Basic elements were grouped, simulated, and macro elements were derived. Macro elements were applied in the simulated production of 100 portions of each entrée formula. Total production time for each formula and average production time for each entrée classification were calculated. Application of macro elements indicated that this method of predetermining production time was feasible and could be adapted by quantity foodservice managers as a decision technique used to evaluate menu mix, production personnel schedules, and allocation of equipment usage. These macro elements could serve as a basis for further development and refinement of other macro elements which could be applied to a variety of menu item formulas.

Non-coding, mRNA-like RNAs database Y2K

PubMed Central

Erdmann, Volker A.; Szymanski, Maciej; Hochberg, Abraham; Groot, Nathan de; Barciszewski, Jan

2000-01-01

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www.man.poznan.pl/5SData/ncRNA/index.html PMID:10592224

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

PubMed Central

Laurent, Georges St.; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J.L.; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R.R.; Nicolas, Estelle; McCaffrey, Timothy A.; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-01-01

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in cis to activate nearby genes. This effect while most pronounced in closely spaced vlincRNA–gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlincRNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. PMID:27001520

Crosstalk between the Notch signaling pathway and non-coding RNAs in gastrointestinal cancers

PubMed Central

Pan, Yangyang; Mao, Yuyan; Jin, Rong; Jiang, Lei

2018-01-01

The Notch signaling pathway is one of the main signaling pathways that mediates direct contact between cells, and is essential for normal development. It regulates various cellular processes, including cell proliferation, apoptosis, migration, invasion, angiogenesis and metastasis. It additionally serves an important function in tumor progression. Non-coding RNAs mainly include small microRNAs, long non-coding RNAs and circular RNAs. At present, a large body of literature supports the biological significance of non-coding RNAs in tumor progression. It is also becoming increasingly evident that cross-talk exists between Notch signaling and non-coding RNAs. The present review summarizes the current knowledge of Notch-mediated gastrointestinal cancer cell processes, and the effect of the crosstalk between the three major types of non-coding RNAs and the Notch signaling pathway on the fate of gastrointestinal cancer cells. PMID:29285185

Dietary Intervention by Phytochemicals and Their Role in Modulating Coding and Non-Coding Genes in Cancer

PubMed Central

Budisan, Liviuta; Gulei, Diana; Zanoaga, Oana Mihaela; Irimie, Alexandra Iulia; Chira, Sergiu; Braicu, Cornelia; Gherman, Claudia Diana; Berindan-Neagoe, Ioana

2017-01-01

Phytochemicals are natural compounds synthesized as secondary metabolites in plants, representing an important source of molecules with a wide range of therapeutic applications. These natural agents are important regulators of key pathological processes/conditions, including cancer, as they are able to modulate the expression of coding and non-coding transcripts with an oncogenic or tumour suppressor role. These natural agents are currently exploited for the development of therapeutic strategies alone or in tandem with conventional treatments for cancer. The aim of this paper is to review the recent studies regarding the role of these natural phytochemicals in different processes related to cancer inhibition, including apoptosis activation, angiogenesis and metastasis suppression. From the large palette of phytochemicals we selected epigallocatechin gallate (EGCG), caffeic acid phenethyl ester (CAPE), genistein, morin and kaempferol, due to their increased activity in modulating multiple coding and non-coding genes, targeting the main hallmarks of cancer. PMID:28587155

Dietary Intervention by Phytochemicals and Their Role in Modulating Coding and Non-Coding Genes in Cancer.

PubMed

Budisan, Liviuta; Gulei, Diana; Zanoaga, Oana Mihaela; Irimie, Alexandra Iulia; Sergiu, Chira; Braicu, Cornelia; Gherman, Claudia Diana; Berindan-Neagoe, Ioana

2017-06-01

Phytochemicals are natural compounds synthesized as secondary metabolites in plants, representing an important source of molecules with a wide range of therapeutic applications. These natural agents are important regulators of key pathological processes/conditions, including cancer, as they are able to modulate the expression of coding and non-coding transcripts with an oncogenic or tumour suppressor role. These natural agents are currently exploited for the development of therapeutic strategies alone or in tandem with conventional treatments for cancer. The aim of this paper is to review the recent studies regarding the role of these natural phytochemicals in different processes related to cancer inhibition, including apoptosis activation, angiogenesis and metastasis suppression. From the large palette of phytochemicals we selected epigallocatechin gallate (EGCG), caffeic acid phenethyl ester (CAPE), genistein, morin and kaempferol, due to their increased activity in modulating multiple coding and non-coding genes, targeting the main hallmarks of cancer.

21 CFR 607.65 - Exemptions for blood product establishments.

Code of Federal Regulations, 2012 CFR

2012-04-01

... for further manufacturing use, or preparation of red blood cells for transfusion are not acts... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Exemptions for blood product establishments. 607... BLOOD AND BLOOD PRODUCTS Exemptions § 607.65 Exemptions for blood product establishments. The following...

21 CFR 607.65 - Exemptions for blood product establishments.

Code of Federal Regulations, 2013 CFR

2013-04-01

... for further manufacturing use, or preparation of red blood cells for transfusion are not acts... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Exemptions for blood product establishments. 607... BLOOD AND BLOOD PRODUCTS Exemptions § 607.65 Exemptions for blood product establishments. The following...

21 CFR 607.65 - Exemptions for blood product establishments.

Code of Federal Regulations, 2014 CFR

2014-04-01

... for further manufacturing use, or preparation of red blood cells for transfusion are not acts... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Exemptions for blood product establishments. 607... BLOOD AND BLOOD PRODUCTS Exemptions § 607.65 Exemptions for blood product establishments. The following...

21 CFR 607.65 - Exemptions for blood product establishments.

Code of Federal Regulations, 2010 CFR

2010-04-01

... for further manufacturing use, or preparation of red blood cells for transfusion are not acts... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Exemptions for blood product establishments. 607... BLOOD AND BLOOD PRODUCTS Exemptions § 607.65 Exemptions for blood product establishments. The following...

21 CFR 207.7 - Establishment registration and product listing for human blood and blood products and for medical...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Establishment registration and product listing for human blood and blood products and for medical devices. 207.7 Section 207.7 Food and Drugs FOOD AND DRUG... Repository Team (HFD-143), Center for Drug Evaluation and Research, FDA, and list their drug products in...

21 CFR 207.7 - Establishment registration and product listing for human blood and blood products and for medical...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Establishment registration and product listing for human blood and blood products and for medical devices. 207.7 Section 207.7 Food and Drugs FOOD AND DRUG... Repository Team (HFD-143), Center for Drug Evaluation and Research, FDA, and list their drug products in...

Non-coding RNAs and Berberine: A new mechanism of its anti-diabetic activities.

PubMed

Chang, Wenguang

2017-01-15

Type 2 Diabetes (T2D) is a metabolic disease with high mortality and morbidity. Non-coding RNAs, including small and long non-coding RNAs, are a novel class of functional RNA molecules that regulate multiple biological functions through diverse mechanisms. Studies in the last decade have demonstrated that non-coding RNAs may represent compelling therapeutic targets and play important roles in regulating the course of insulin resistance and T2D. Berberine, a plant-based alkaloid, has shown promise as an anti-hyperglycaemic, anti-hyperlipidaemic agent against T2D. Previous studies have primarily focused on a diverse array of efficacy end points of berberine in the pathogenesis of metabolic syndromes and inflammation or oxidative stress. Currently, an increasing number of studies have revealed the importance of non-coding RNAs as regulators of the anti-diabetic effects of berberine. The regulation of non-coding RNAs has been associated with several therapeutic actions of berberine in T2D progression. Thus, this review summarizes the anti-diabetic mechanisms of berberine by focusing on its role in regulating non-coding RNA, thus demonstrating that berberine exerts global anti-diabetic effects by targeting non-coding RNAs and that these effects involve several miRNAs, lncRNAs and multiple signal pathways, which may enhance the current understanding of the anti-diabetic mechanism actions of berberine and provide new pathological targets for the development of berberine-related drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

A benchmark study of scoring methods for non-coding mutations.

PubMed

Drubay, Damien; Gautheret, Daniel; Michiels, Stefan

2018-05-15

Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance. We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases). Using the ClinVar benchmark, CADD was the best tool for detecting the pathogenic variants that are mainly located in protein coding gene regions. Using the COSMIC benchmark, FATHMM-MKL, GWAVA and SOMliver outperformed the other tools for pathogenic variants that are typically located in lincRNAs, pseudogenes and other parts of the non-coding genome. However, all tools had low precision, which could potentially be improved by future non-coding genome feature discoveries. These results may have been influenced by the presence of potential benign variants in the COSMIC database. The development of a gold standard as consistent as ClinVar for these regions will be necessary to confirm our tool ranking. The Snakemake, C++ and R codes are freely available from https://github.com/Oncostat/BenchmarkNCVTools and supported on Linux. damien.drubay@gustaveroussy.fr or stefan.michiels@gustaveroussy.fr. Supplementary data are available at Bioinformatics online.

Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs

PubMed Central

Cheng, Chao; Ung, Matthew; Grant, Gavin D.; Whitfield, Michael L.

2013-01-01

Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division. The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements. PMID:23874175

Citrate metabolism and its complications in non-massive blood transfusions: association with decompensated metabolic alkalosis+respiratory acidosis and serum electrolyte levels.

PubMed

Bıçakçı, Zafer; Olcay, Lale

2014-06-01

Metabolic alkalosis, which is a non-massive blood transfusion complication, is not reported in the literature although metabolic alkalosis dependent on citrate metabolism is reported to be a massive blood transfusion complication. The aim of this study was to investigate the effect of elevated carbon dioxide production due to citrate metabolism and serum electrolyte imbalance in patients who received frequent non-massive blood transfusions. Fifteen inpatients who were diagnosed with different conditions and who received frequent blood transfusions (10-30 ml/kg/day) were prospectively evaluated. Patients who had initial metabolic alkalosis (bicarbonate>26 mmol/l), who needed at least one intensive blood transfusion in one-to-three days for a period of at least 15 days, and whose total transfusion amount did not fit the massive blood transfusion definition (<80 ml/kg) were included in the study. The estimated mean total citrate administered via blood and blood products was calculated as 43.2 ± 34.19 mg/kg/day (a total of 647.70 mg/kg in 15 days). Decompensated metabolic alkalosis+respiratory acidosis developed as a result of citrate metabolism. There was a positive correlation between cumulative amount of citrate and the use of fresh frozen plasma, venous blood pH, ionized calcium, serum-blood gas sodium and mortality, whereas there was a negative correlation between cumulative amount of citrate and serum calcium levels, serum phosphorus levels and amount of urine chloride. In non-massive, but frequent blood transfusions, elevated carbon dioxide production due to citrate metabolism causes intracellular acidosis. As a result of intracellular acidosis compensation, decompensated metabolic alkalosis+respiratory acidosis and electrolyte imbalance may develop. This situation may contribute to the increase in mortality. In conclusion, it should be noted that non-massive, but frequent blood transfusions may result in certain complications. Copyright © 2014 Elsevier Ltd

A Catalogue of Putative cis-Regulatory Interactions Between Long Non-coding RNAs and Proximal Coding Genes Based on Correlative Analysis Across Diverse Human Tumors.

PubMed

Basu, Swaraj; Larsson, Erik

2018-05-31

Antisense transcripts and other long non-coding RNAs are pervasive in mammalian cells, and some of these molecules have been proposed to regulate proximal protein-coding genes in cis For example, non-coding transcription can contribute to inactivation of tumor suppressor genes in cancer, and antisense transcripts have been implicated in the epigenetic inactivation of imprinted genes. However, our knowledge is still limited and more such regulatory interactions likely await discovery. Here, we make use of available gene expression data from a large compendium of human tumors to generate hypotheses regarding non-coding-to-coding cis -regulatory relationships with emphasis on negative associations, as these are less likely to arise for reasons other than cis -regulation. We document a large number of possible regulatory interactions, including 193 coding/non-coding pairs that show expression patterns compatible with negative cis -regulation. Importantly, by this approach we capture several known cases, and many of the involved coding genes have known roles in cancer. Our study provides a large catalog of putative non-coding/coding cis -regulatory pairs that may serve as a basis for further experimental validation and characterization. Copyright © 2018 Basu and Larsson.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity.

PubMed

Hrdlickova, Barbara; Kumar, Vinod; Kanduri, Kartiek; Zhernakova, Daria V; Tripathi, Subhash; Karjalainen, Juha; Lund, Riikka J; Li, Yang; Ullah, Ubaid; Modderman, Rutger; Abdulahad, Wayel; Lähdesmäki, Harri; Franke, Lude; Lahesmaa, Riitta; Wijmenga, Cisca; Withoff, Sebo

2014-01-01

Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID), our understanding of the disease mechanisms is still limited. In particular, more than 90% of the risk variants lie in non-coding regions, and almost 10% of these map to long non-coding RNA transcripts (lncRNAs). lncRNAs are known to show more cell-type specificity than protein-coding genes. We aimed to characterize lncRNAs and protein-coding genes located in loci associated with nine AIDs which have been well-defined by Immunochip analysis and by transcriptome analysis across seven populations of peripheral blood leukocytes (granulocytes, monocytes, natural killer (NK) cells, B cells, memory T cells, naive CD4(+) and naive CD8(+) T cells) and four populations of cord blood-derived T-helper cells (precursor, primary, and polarized (Th1, Th2) T-helper cells). We show that lncRNAs mapping to loci shared between AID are significantly enriched in immune cell types compared to lncRNAs from the whole genome (α <0.005). We were not able to prioritize single cell types relevant for specific diseases, but we observed five different cell types enriched (α <0.005) in five AID (NK cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, and psoriasis; memory T and CD8(+) T cells in juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis; Th0 and Th2 cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis). Furthermore, we show that co-expression analyses of lncRNAs and protein-coding genes can predict the signaling pathways in which these AID-associated lncRNAs are involved. The observed enrichment of lncRNA transcripts in AID loci implies lncRNAs play an important role in AID etiology and suggests that lncRNA genes should be studied in more detail to interpret GWAS

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

PubMed

St Laurent, Georges; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J L; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Nicolas, Estelle; McCaffrey, Timothy A; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-04-20

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Numerical simulation of the non-Newtonian blood flow through a mechanical aortic valve. Non-Newtonian blood flow in the aortic root

NASA Astrophysics Data System (ADS)

De Vita, F.; de Tullio, M. D.; Verzicco, R.

2016-04-01

This work focuses on the comparison between Newtonian and non-Newtonian blood flows through a bileaflet mechanical heart valve in the aortic root. The blood, in fact, is a concentrated suspension of cells, mainly red blood cells, in a Newtonian matrix, the plasma, and consequently its overall behavior is that of a non-Newtonian fluid owing to the action of the cells' membrane on the fluid part. The common practice, however, assumes the blood in large vessels as a Newtonian fluid since the shear rate is generally high and the effective viscosity becomes independent of the former. In this paper, we show that this is not always the case even in the aorta, the largest artery of the systemic circulation, owing to the pulsatile and transitional nature of the flow. Unexpectedly, for most of the pulsating cycle and in a large part of the fluid volume, the shear rate is smaller than the threshold level for the blood to display a constant effective viscosity and its shear thinning character might affect the system dynamics. A direct inspection of the various flow features has shown that the valve dynamics, the transvalvular pressure drop and the large-scale features of the flow are very similar for the Newtonian and non-Newtonian fluid models. On the other hand, the mechanical damage of the red blood cells (hemolysis), induced by the altered stress values in the flow, is larger for the non-Newtonian fluid model than for the Newtonian one.

Non-binary LDPC-coded modulation for high-speed optical metro networks with backpropagation

NASA Astrophysics Data System (ADS)

Arabaci, Murat; Djordjevic, Ivan B.; Saunders, Ross; Marcoccia, Roberto M.

2010-01-01

To simultaneously mitigate the linear and nonlinear channel impairments in high-speed optical communications, we propose the use of non-binary low-density-parity-check-coded modulation in combination with a coarse backpropagation method. By employing backpropagation, we reduce the memory in the channel and in return obtain significant reductions in the complexity of the channel equalizer which is exponentially proportional to the channel memory. We then compensate for the remaining channel distortions using forward error correction based on non-binary LDPC codes. We propose non-binary-LDPC-coded modulation scheme because, compared to bit-interleaved binary-LDPC-coded modulation scheme employing turbo equalization, the proposed scheme lowers the computational complexity and latency of the overall system while providing impressively larger coding gains.

Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes

PubMed Central

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U.; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N.; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O.

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

PubMed

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

Illumination-compensated non-contact imaging photoplethysmography via dual-mode temporally coded illumination

NASA Astrophysics Data System (ADS)

Amelard, Robert; Scharfenberger, Christian; Wong, Alexander; Clausi, David A.

2015-03-01

Non-contact camera-based imaging photoplethysmography (iPPG) is useful for measuring heart rate in conditions where contact devices are problematic due to issues such as mobility, comfort, and sanitation. Existing iPPG methods analyse the light-tissue interaction of either active or passive (ambient) illumination. Many active iPPG methods assume the incident ambient light is negligible to the active illumination, resulting in high power requirements, while many passive iPPG methods assume near-constant ambient conditions. These assumptions can only be achieved in environments with controlled illumination and thus constrain the use of such devices. To increase the number of possible applications of iPPG devices, we propose a dual-mode active iPPG system that is robust to changes in ambient illumination variations. Our system uses a temporally-coded illumination sequence that is synchronized with the camera to measure both active and ambient illumination interaction for determining heart rate. By subtracting the ambient contribution, the remaining illumination data can be attributed to the controlled illuminant. Our device comprises a camera and an LED illuminant controlled by a microcontroller. The microcontroller drives the temporal code via synchronizing the frame captures and illumination time at the hardware level. By simulating changes in ambient light conditions, experimental results show our device is able to assess heart rate accurately in challenging lighting conditions. By varying the temporal code, we demonstrate the trade-off between camera frame rate and ambient light compensation for optimal blood pulse detection.

50 CFR Table 14b to Part 679 - Port of Landing Codes: Non-Alaska

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Port of Landing Codes: Non-Alaska 14b... ALASKA Pt. 679, Table 14b Table 14b to Part 679—Port of Landing Codes: Non-Alaska (California, Canada... report a landing at a location not currently assigned a location code number, use the code for “Other...

50 CFR Table 14b to Part 679 - Port of Landing Codes: Non-Alaska

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Port of Landing Codes: Non-Alaska 14b... ALASKA Pt. 679, Table 14b Table 14b to Part 679—Port of Landing Codes: Non-Alaska (California, Canada... report a landing at a location not currently assigned a location code number, use the code for “Other...

Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

PubMed Central

2012-01-01

Background Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, the accuracies of previous methods of finding borders based on entropy segmentation method still need to be improved. Methods In this study, we first applied a new recursive entropic segmentation method on DNA sequences to get preliminary significant cuts. A 22-symbol alphabet is used to capture the differential composition of nucleotide doublets and stop codon patterns along three phases in both DNA strands. This process requires no prior training datasets. Results Comparing with the previous segmentation methods, the experimental results on three bacteria genomes, Rickettsia prowazekii, Borrelia burgdorferi and E.coli, show that our approach improves the accuracy for finding the borders between coding and non-coding regions in DNA sequences. Conclusions This paper presents a new segmentation method in prokaryotes based on Jensen-Rényi divergence with a 22-symbol alphabet. For three bacteria genomes, comparing to A12_JR method, our method raised the accuracy of finding the borders between protein coding and non-coding regions in DNA sequences. PMID:23282225

An expanding universe of the non-coding genome in cancer biology.

PubMed

Xue, Bin; He, Lin

2014-06-01

Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Capacity achieving nonbinary LDPC coded non-uniform shaping modulation for adaptive optical communications.

PubMed

Lin, Changyu; Zou, Ding; Liu, Tao; Djordjevic, Ivan B

2016-08-08

A mutual information inspired nonbinary coded modulation design with non-uniform shaping is proposed. Instead of traditional power of two signal constellation sizes, we design 5-QAM, 7-QAM and 9-QAM constellations, which can be used in adaptive optical networks. The non-uniform shaping and LDPC code rate are jointly considered in the design, which results in a better performance scheme for the same SNR values. The matched nonbinary (NB) LDPC code is used for this scheme, which further improves the coding gain and the overall performance. We analyze both coding performance and system SNR performance. We show that the proposed NB LDPC-coded 9-QAM has more than 2dB gain in symbol SNR compared to traditional LDPC-coded star-8-QAM. On the other hand, the proposed NB LDPC-coded 5-QAM and 7-QAM have even better performance than LDPC-coded QPSK.

Bar code-based pre-transfusion check in pre-operative autologous blood donation.

PubMed

Ohsaka, Akimichi; Furuta, Yoshiaki; Ohsawa, Toshiya; Kobayashi, Mitsue; Abe, Katsumi; Inada, Eiichi

2010-10-01

The objective of this study was to demonstrate the feasibility of a bar code-based identification system for the pre-transfusion check at the bedside in the setting of pre-operative autologous blood donation (PABD). Between July 2003 and December 2008 we determined the compliance rate and causes of failure of electronic bedside checking for PABD transfusion. A total of 5627 (9% of all transfusions) PABD units were administered without a single mistransfusion. The overall rate of compliance with electronic checking was 99%. The bar code-based identification system was applicable to the pre-transfusion check for PABD transfusion. Copyright © 2010 Elsevier Ltd. All rights reserved.

Design of ACM system based on non-greedy punctured LDPC codes

NASA Astrophysics Data System (ADS)

Lu, Zijun; Jiang, Zihong; Zhou, Lin; He, Yucheng

2017-08-01

In this paper, an adaptive coded modulation (ACM) scheme based on rate-compatible LDPC (RC-LDPC) codes was designed. The RC-LDPC codes were constructed by a non-greedy puncturing method which showed good performance in high code rate region. Moreover, the incremental redundancy scheme of LDPC-based ACM system over AWGN channel was proposed. By this scheme, code rates vary from 2/3 to 5/6 and the complication of the ACM system is lowered. Simulations show that more and more obvious coding gain can be obtained by the proposed ACM system with higher throughput.

Non-coding RNAs and Their Roles in Stress Response in Plants.

PubMed

Wang, Jingjing; Meng, Xianwen; Dobrovolskaya, Oxana B; Orlov, Yuriy L; Chen, Ming

2017-10-01

Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

Standing your Ground to Exoribonucleases: Function of Flavivirus Long Non-coding RNAs

PubMed Central

Charley, Phillida A.; Wilusz, Jeffrey

2015-01-01

Members of the Flaviviridae (e.g. Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomicflavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis. PMID:26368052

Spine tumor resection among patients who refuse blood product transfusion: a retrospective case series.

PubMed

Kisilevsky, Alexandra E; Stobart, Liam; Roland, Kristine; Flexman, Alana M

2016-12-01

To describe the perioperative blood conservation strategies and postoperative outcomes in patients who undergo complex spinal surgery for tumor resection and who also refuse blood product transfusion. A retrospective case series. A single-center, tertiary care and academic teaching hospital in Canada. All adult patients undergoing elective major spine tumor resection and refusing blood product transfusion who were referred to our institutional Blood Utilization Program between June 1, 2004, and May 9, 2014. Data on the use of iron, erythropoietin, preoperative autologous blood donation, acute normovolemic hemodilution, antifibrinolytic therapy, cell salvage, intraoperative hypotension, and active warming techniques were collected. Data on perioperative hemoglobin nadir, adverse outcomes, and hospital length of stay were also collected. Four patients who refused blood transfusion (self-identified as Jehovah's Witnesses) underwent non-emergent complex spine surgery for recurrent chondrosarcoma, meningioma, metastatic adenocarcinoma, and metastatic malignant melanoma. All patients received 1 or more perioperative blood conservation strategy including preoperative iron and/or erythropoietin, intraoperative antifibrinolytic therapy, and cell salvage. No patients experienced severe perioperative anemia (average hemoglobin nadir, 124 g/L) or anemia-related postoperative complications. Patients who decline blood product transfusion can successfully undergo major spine tumor resection. Careful patient selection and timely referral for perioperative optimization such that the risk of severe anemia is minimized are important for success. Copyright © 2016 Elsevier Inc. All rights reserved.

u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

NASA Astrophysics Data System (ADS)

Gao, Jian; Wang, Yongkang

2018-01-01

Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

Update on the use of blood and blood products in ruminants.

PubMed

Balcomb, Christie; Foster, Derek

2014-07-01

The use of whole blood and/or blood products is indicated in ruminant medicine. The goal of this article is to summarize previous literature on blood groups in ruminants and camelids, list indications for transfusion, and describe collection and transfusion techniques applicable to small ruminants and cattle that can be used in practice. Copyright © 2014 Elsevier Inc. All rights reserved.

Long non-coding RNA expression profile in cervical cancer tissues

PubMed Central

Zhu, Hua; Chen, Xiangjian; Hu, Yan; Shi, Zhengzheng; Zhou, Qing; Zheng, Jingjie; Wang, Yifeng

2017-01-01

Cervical cancer (CC), one of the most common types of cancer of the female population, presents an enormous challenge in diagnosis and treatment. Long non-coding (lnc)RNAs, non-coding (nc)RNAs with length >200 nucleotides, have been identified to be associated with multiple types of cancer, including CC. This class of nc transcripts serves an important role in tumor suppression and oncogenic signaling pathways. In the present study, the microarray method was used to obtain the expression profile of lncRNAs and protein-coding mRNAs and to compare the expression of lncRNAs between CC tissues and corresponding adjacent non-cancerous tissues in order to screen potential lncRNAs for associations with CC. Overall, 3356 lncRNAs with significantly different expression pattern in CC tissues compared with adjacent non-cancerous tissues were identified, while 1,857 of them were upregulated. These differentially expressed lncRNAs were additionally classified into 5 subgroups. Reverse transcription quantitative polymerase chain reactions were performed to validate the expression pattern of 5 random selected lncRNAs, and 2lncRNAs were identified to have significantly different expression in CC samples compared with adjacent non-cancerous tissues. This finding suggests that those lncRNAs with different expression may serve important roles in the development of CC, and the expression data may provide information for additional study on the involvement of lncRNAs in CC. PMID:28789353

25 CFR 111.2 - Enrolling non-full-blood children.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Enrolling non-full-blood children. 111.2 Section 111.2 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FINANCIAL ACTIVITIES ANNUITY AND OTHER PER CAPITA PAYMENTS § 111.2 Enrolling non-full-blood children. Where an Indian woman was married to a white...

25 CFR 111.2 - Enrolling non-full-blood children.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 1 2014-04-01 2014-04-01 false Enrolling non-full-blood children. 111.2 Section 111.2... CAPITA PAYMENTS § 111.2 Enrolling non-full-blood children. Where an Indian woman was married to a white... though she left it after marriage and lived away from the reservation, the children of such a marriage...

25 CFR 111.2 - Enrolling non-full-blood children.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 25 Indians 1 2012-04-01 2011-04-01 true Enrolling non-full-blood children. 111.2 Section 111.2... CAPITA PAYMENTS § 111.2 Enrolling non-full-blood children. Where an Indian woman was married to a white... though she left it after marriage and lived away from the reservation, the children of such a marriage...

25 CFR 111.2 - Enrolling non-full-blood children.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 false Enrolling non-full-blood children. 111.2 Section 111.2... CAPITA PAYMENTS § 111.2 Enrolling non-full-blood children. Where an Indian woman was married to a white... though she left it after marriage and lived away from the reservation, the children of such a marriage...

25 CFR 111.2 - Enrolling non-full-blood children.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 1 2013-04-01 2013-04-01 false Enrolling non-full-blood children. 111.2 Section 111.2... CAPITA PAYMENTS § 111.2 Enrolling non-full-blood children. Where an Indian woman was married to a white... though she left it after marriage and lived away from the reservation, the children of such a marriage...

Splitting blood and blood product packaging reduces donor exposure for patients undergoing cardiopulmonary bypass.

PubMed

Nuszkowski, M M; Jonas, R A; Zurakowski, D; Deutsch, N

2015-11-01

Cardiopulmonary bypass for congenital heart surgery requires packed red cells (PRBC) and fresh frozen plasma (FFP) to be available, both for priming of the circuit as well as to replace blood loss. This study examines the hypothesis that splitting one unit of packed red blood cells and one unit of fresh frozen plasma into two half units reduces blood product exposure and wastage in the Operating Room. Beginning August 2013, the blood bank at Children's National Medical Center began splitting one unit of packed red blood cells (PRBC) and one unit of fresh frozen plasma (FFP) for patients undergoing cardiopulmonary bypass (CPB). The 283 patients who utilized CPB during calendar year 2013 were divided into 2 study groups: before the split and after the split. The principal endpoints were blood product usage and donor exposure intra-operatively and within 72 hours post-operatively. There was a significant decrease in median total donor exposures for FFP and cryoprecipitate from 5 to 4 per case (p = 0.007, Mann-Whitney U-test). However, there was no difference in the volume of blood and blood products used; in fact, there was a significant increase in the amount of FFP that was wasted with the switch to splitting the unit of FFP. We found that modification of blood product packaging can decrease donor exposure. Future investigation is needed as to how to modify packaging to minimize wastage. © The Author(s) 2015.

Long Non-Coding RNA Malat1 Regulates Angiogenesis in Hindlimb Ischemia.

PubMed

Zhang, Xuejing; Tang, Xuelian; Hamblin, Milton H; Yin, Ke-Jie

2018-06-11

Angiogenesis is a complex process that depends on the delicate regulation of gene expression. Dysregulation of transcription during angiogenesis often leads to various human diseases. Emerging evidence has recently begun to show that long non-coding RNAs (lncRNAs) may mediate angiogenesis in both physiological and pathological conditions; concurrently, underlying molecular mechanisms are largely unexplored. Previously, our lab identified metastasis associates lung adenocarcinoma transcript 1 ( Malat1 ) as an oxygen-glucose deprivation (OGD)-responsive endothelial lncRNA. Here we reported that genetic deficiency of Malat1 leads to reduced blood vessel formation and local blood flow perfusion in mouse hind limbs at one to four weeks after hindlimb ischemia. Malat1 and vascular endothelial growth factor receptor 2 ( VEGFR2 ) levels were found to be increased in both cultured mouse primary skeletal muscle microvascular endothelial cells (SMMECs) after 16 h OGD followed by 24 h reperfusion and in mouse gastrocnemius muscle that underwent hindlimb ischemia followed by 28 days of reperfusion. Moreover, Malat1 silencing by locked nucleic acid (LNA)-GapmeRs significantly reduced tube formation, cell migration, and cell proliferation in SMMEC cultures. Mechanistically, RNA subcellular isolation and RNA-immunoprecipitation experiments demonstrate that Malat1 directly targets VEGFR2 to facilitate angiogenesis. The results suggest that Malat1 regulates cell-autonomous angiogenesis through direct regulation of VEGFR2.

Examining the relationship between comprehension and production processes in code-switched language.

PubMed

Guzzardo Tamargo, Rosa E; Valdés Kroff, Jorge R; Dussias, Paola E

2016-08-01

We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish-English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants' comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension.

Examining the relationship between comprehension and production processes in code-switched language

PubMed Central

Guzzardo Tamargo, Rosa E.; Valdés Kroff, Jorge R.; Dussias, Paola E.

2016-01-01

We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish–English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants’ comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension. PMID:28670049

Quantum Kronecker sum-product low-density parity-check codes with finite rate

NASA Astrophysics Data System (ADS)

Kovalev, Alexey A.; Pryadko, Leonid P.

2013-07-01

We introduce an ansatz for quantum codes which gives the hypergraph-product (generalized toric) codes by Tillich and Zémor and generalized bicycle codes by MacKay as limiting cases. The construction allows for both the lower and the upper bounds on the minimum distance; they scale as a square root of the block length. Many thus defined codes have a finite rate and limited-weight stabilizer generators, an analog of classical low-density parity-check (LDPC) codes. Compared to the hypergraph-product codes, hyperbicycle codes generally have a wider range of parameters; in particular, they can have a higher rate while preserving the estimated error threshold.

Dengue Non-coding RNA: TRIMmed for Transmission.

PubMed

Göertz, Giel P; Pijlman, Gorben P

2015-08-12

Dengue virus RNA is trimmed by the 5'→3' exoribonuclease XRN1 to produce an abundant, non-coding subgenomic flavivirus RNA (sfRNA) in infected cells. In a recent paper in Science, Manokaran et al. (2015) report that sfRNA binds TRIM25 to evade innate immune sensing of viral RNA by RIG-I. Copyright © 2015 Elsevier Inc. All rights reserved.

The fast non-LTE code DEDALE

NASA Astrophysics Data System (ADS)

Gilleron, Franck; Piron, Robin

2015-12-01

We present Dédale, a fast code implementing a simplified non-local-thermodynamic-equilibrium (NLTE) plasma model. In this approach, the stationary collisional-radiative rates equations are solved for a set of well-chosen Layzer complexes in order to determine the ion state populations. The electronic structure is approximated using the screened hydrogenic model (SHM) of More with relativistic corrections. The radiative and collisional cross-sections are based on Kramers and Van Regemorter formula, respectively, which are extrapolated to derive analytical expressions for all the rates. The latter are improved thereafter using Gaunt factors or more accurate tabulated data. Special care is taken for dielectronic rates which are compared and rescaled with quantum calculations from the Averroès code. The emissivity and opacity spectra are calculated under the same assumptions as for the radiative rates, either in a detailed manner by summing the transitions between each pair of complexes, or in a coarser statistical way by summing the one-electron transitions averaged over the complexes. Optionally, nℓ-splitting can be accounted for using a WKB approach in an approximate potential reconstructed analytically from the screened charges. It is also possible to improve the spectra by replacing some transition arrays with more accurate data tabulated using the SCO-RCG or FAC codes. This latter option is particularly useful for K-shell emission spectroscopy. The Dédale code was used to submit neon and tungsten cases in the last NLTE-8 workshop (Santa Fe, November 4-8, 2013). Some of these results are presented, as well as comparisons with Averroès calculations.

Small non-coding RNAs in streptomycetes.

PubMed

Heueis, Nona; Vockenhuber, Michael-Paul; Suess, Beatrix

2014-01-01

Streptomycetes are Gram-positive, GC-rich, soil dwelling bacteria, occurring ubiquitary throughout nature. They undergo extensive morphological changes from spores to filamentous mycelia and produce a plethora of secondary metabolites. Owing to their complex life cycle, streptomycetes require efficient regulatory machinery for the control of gene expression. Therefore, they possess a large diversity of regulators. Within this review we summarize the current knowledge about the importance of small non-coding RNA for the control of gene expression in these organisms.

Phonological Codes Constrain Output of Orthographic Codes via Sublexical and Lexical Routes in Chinese Written Production

PubMed Central

Wang, Cheng; Zhang, Qingfang

2015-01-01

To what extent do phonological codes constrain orthographic output in handwritten production? We investigated how phonological codes constrain the selection of orthographic codes via sublexical and lexical routes in Chinese written production. Participants wrote down picture names in a picture-naming task in Experiment 1or response words in a symbol—word associative writing task in Experiment 2. A sublexical phonological property of picture names (phonetic regularity: regular vs. irregular) in Experiment 1and a lexical phonological property of response words (homophone density: dense vs. sparse) in Experiment 2, as well as word frequency of the targets in both experiments, were manipulated. A facilitatory effect of word frequency was found in both experiments, in which words with high frequency were produced faster than those with low frequency. More importantly, we observed an inhibitory phonetic regularity effect, in which low-frequency picture names with regular first characters were slower to write than those with irregular ones, and an inhibitory homophone density effect, in which characters with dense homophone density were produced more slowly than those with sparse homophone density. Results suggested that phonological codes constrained handwritten production via lexical and sublexical routes. PMID:25879662

Proper coding of the Abbreviated Injury Scale: can clinical parameters help as surrogates in estimating blood loss?

PubMed

Burkhardt, M; Holstein, J H; Moersdorf, P; Kristen, A; Lefering, R; Pohlemann, T; Pizanis, A

2014-08-01

The Abbreviated Injury Scale (AIS) requires the estimation of the lost blood volume for some severity assignments. This study aimed to develop a rule of thumb for facilitating AIS coding by using objective clinical parameters as surrogate markers of blood loss. Using the example of pelvic ring fractures, a retrospective analysis of TraumaRegister DGU(®) data from 2002 to 2011 was performed. As potential surrogate markers of blood loss, we recorded the hemoglobin (Hb) level, systolic blood pressure (SBP), base excess (BE), Quick's value, units of packed red blood cells (PRBCs) transfused before intensive care unit (ICU) admission, and mortality within 24 h. We identified 11,574 patients with pelvic ring fractures (Tile/OTA classification: 39 % type A, 40 % type B, 21 % type C). Type C fractures were 73.1 % AISpelvis 4 and 26.9 % AISpelvis 5. Type B fractures were 47 % AISpelvis 3, 47 % AISpelvis 4, and 6 % AISpelvis 5. In type C fractures, cut-off values of <7 g/dL Hb, <90 mmHg SBP, <-9 mmol/L BE, <35 % Quick's value, >15 units PRBCs, and death within 24 h had a positive predictive value of 47 % and a sensitivity of 62 % for AISpelvis 5. In type B fractures, these cut-off values had poor sensitivity (48 %) and positive predictive value (11 %) for AISpelvis 5. We failed to develop a rule of thumb for facilitating a proper future AIS coding using the example of pelvic ring fractures. The estimation of blood loss for severity assignment still remains a noteworthy weakness in the AIS coding of traumatic injuries.

Energy Cost Impact of Non-Residential Energy Code Requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jian; Hart, Philip R.; Rosenberg, Michael I.

2016-08-22

The 2012 International Energy Conservation Code contains 396 separate requirements applicable to non-residential buildings; however, there is no systematic analysis of the energy cost impact of each requirement. Consequently, limited code department budgets for plan review, inspection, and training cannot be focused on the most impactful items. An inventory and ranking of code requirements based on their potential energy cost impact is under development. The initial phase focuses on office buildings with simple HVAC systems in climate zone 4C. Prototype building simulations were used to estimate the energy cost impact of varying levels of non-compliance. A preliminary estimate of themore » probability of occurrence of each level of non-compliance was combined with the estimated lost savings for each level to rank the requirements according to expected savings impact. The methodology to develop and refine further energy cost impacts, specific to building type, system type, and climate location is demonstrated. As results are developed, an innovative alternative method for compliance verification can focus efforts so only the most impactful requirements from an energy cost perspective are verified for every building and a subset of the less impactful requirements are verified on a random basis across a building population. The results can be further applied in prioritizing training material development and specific areas of building official training.« less

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs

PubMed Central

2014-01-01

Background The genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays. Results We found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed. Conclusions It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events. PMID:24594072

The Hippo pathway in hepatocellular carcinoma: Non-coding RNAs in action.

PubMed

Shi, Xuan; Zhu, Hai-Rong; Liu, Tao-Tao; Shen, Xi-Zhong; Zhu, Ji-Min

2017-08-01

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the third leading cause of cancer-related death worldwide. However, current strategies curing HCC are far from satisfaction. The Hippo pathway is an evolutionarily conserved tumor suppressive pathway that plays crucial roles in organ size control and tissue homeostasis. Its dysregulation is commonly observed in various types of cancer including HCC. Recently, the prominent role of non-coding RNAs in the Hippo pathway during normal development and neoplastic progression is also emerging in liver. Thus, further investigation into the regulatory network between non-coding RNAs and the Hippo pathway and their connections with HCC may provide new therapeutic avenues towards developing an effective preventative or perhaps curative treatment for HCC. Herein we summarize the role of non-coding RNAs in the Hippo pathway, with an emphasis on their contribution to carcinogenesis, diagnosis, treatment and prognosis of HCC. Copyright © 2017 Elsevier B.V. All rights reserved.

GPU Optimizations for a Production Molecular Docking Code*

PubMed Central

Landaverde, Raphael; Herbordt, Martin C.

2015-01-01

Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users. PMID:26594667

GPU Optimizations for a Production Molecular Docking Code.

PubMed

Landaverde, Raphael; Herbordt, Martin C

2014-09-01

Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users.

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements

PubMed Central

Maliszewska-Olejniczak, Kamila; Gruchota, Julita; Gromadka, Robert; Denby Wilkes, Cyril; Arnaiz, Olivier; Mathy, Nathalie; Duharcourt, Sandra; Bétermier, Mireille; Nowak, Jacek K.

2015-01-01

Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium, and establishes for

21 CFR 607.65 - Exemptions for blood product establishments.

Code of Federal Regulations, 2011 CFR

2011-04-01

... use, or preparation of red blood cells for transfusion are not acts requiring such transfusion... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Exemptions for blood product establishments. 607.65... (CONTINUED) BIOLOGICS ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND...

21 CFR 607.37 - Inspection of establishment registrations and blood product listings.

Code of Federal Regulations, 2014 CFR

2014-04-01

... blood product listings. 607.37 Section 607.37 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.37 Inspection of establishment registrations and blood product listings. (a) A copy of the Form FD-2830 (Blood...

21 CFR 607.37 - Inspection of establishment registrations and blood product listings.

Code of Federal Regulations, 2013 CFR

2013-04-01

... blood product listings. 607.37 Section 607.37 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.37 Inspection of establishment registrations and blood product listings. (a) A copy of the Form FD-2830 (Blood...

21 CFR 607.37 - Inspection of establishment registrations and blood product listings.

Code of Federal Regulations, 2012 CFR

2012-04-01

... blood product listings. 607.37 Section 607.37 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.37 Inspection of establishment registrations and blood product listings. (a) A copy of the Form FD-2830 (Blood...

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

Interplay between cardiac transcription factors and non-coding RNAs in predisposing to atrial fibrillation.

PubMed

Mikhailov, Alexander T; Torrado, Mario

2018-05-12

There is growing evidence that putative gene regulatory networks including cardio-enriched transcription factors, such as PITX2, TBX5, ZFHX3, and SHOX2, and their effector/target genes along with downstream non-coding RNAs can play a potentially important role in the process of adaptive and maladaptive atrial rhythm remodeling. In turn, expression of atrial fibrillation-associated transcription factors is under the control of upstream regulatory non-coding RNAs. This review broadly explores gene regulatory mechanisms associated with susceptibility to atrial fibrillation-with key examples from both animal models and patients-within the context of both cardiac transcription factors and non-coding RNAs. These two systems appear to have multiple levels of cross-regulation and act coordinately to achieve effective control of atrial rhythm effector gene expression. Perturbations of a dynamic expression balance between transcription factors and corresponding non-coding RNAs can provoke the development or promote the progression of atrial fibrillation. We also outline deficiencies in current models and discuss ongoing studies to clarify remaining mechanistic questions. An understanding of the function of transcription factors and non-coding RNAs in gene regulatory networks associated with atrial fibrillation risk will enable the development of innovative therapeutic strategies.

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.

PubMed

Ricaño-Ponce, Isis; Zhernakova, Daria V; Deelen, Patrick; Luo, Oscar; Li, Xingwang; Isaacs, Aaron; Karjalainen, Juha; Di Tommaso, Jennifer; Borek, Zuzanna Agnieszka; Zorro, Maria M; Gutierrez-Achury, Javier; Uitterlinden, Andre G; Hofman, Albert; van Meurs, Joyce; Netea, Mihai G; Jonkers, Iris H; Withoff, Sebo; van Duijn, Cornelia M; Li, Yang; Ruan, Yijun; Franke, Lude; Wijmenga, Cisca; Kumar, Vinod

2016-04-01

Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood samples. We were able to link 71 (39%) of the AID-SNPs to two or more nearby genes, providing evidence that for part of the AID loci multiple causal genes exist. While 54 of the AID loci are shared by one or more AID, 17% of them do not share candidate causal genes. In addition to finding novel genes such as ULK3, we also implicate novel disease mechanisms and pathways like autophagy in celiac disease pathogenesis. Furthermore, 42 of the AID SNPs specifically affected the expression of 53 non-coding RNA genes. To further understand how the non-coding genome contributes to AID, the SNPs were linked to functional regulatory elements, which suggest a model where AID genes are regulated by network of chromatin looping/non-coding RNAs interactions. The looping model also explains how a causal candidate gene is not necessarily the gene closest to the AID SNP, which was the case in nearly 50% of cases. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.

PubMed

Al-Tobasei, Rafet; Paneru, Bam; Salem, Mohamed

2016-01-01

The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer

PubMed Central

Wang, Hongbo; Zhao, Yingchao; Chen, Mingyue; Cui, Jie

2017-01-01

Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16) mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN) tissues from three patients with high-throughput RNA sequencing (RNA-seq). In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE) in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO) terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA) network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer. PMID:28970820

[Computer-assisted management of depots for blood products in health establishments].

PubMed

Carré, J

2008-11-01

To manage the filing of blood components at the hospital of the city of Bayeux, the laboratory uses Cursus, a dedicated software for haemovigilance. Benefits for using this software at different steps of the blood bank management are: simplification, security and harmonization of practices during receipt and issurance of blood components, securing recordings with the use of bar codes for patient identification and blood components listing, implementation of a computerized tracking system for transfusion, traceability, limitation of written documents and availability of statistics on the management of the depot.

21 CFR 20.115 - Product codes for manufacturing or sales dates.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Product codes for manufacturing or sales dates. 20.115 Section 20.115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL PUBLIC INFORMATION Availability of Specific Categories of Records § 20.115 Product codes...

Non-coding RNA in cystic fibrosis.

PubMed

Glasgow, Arlene M A; De Santi, Chiara; Greene, Catherine M

2018-05-09

Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

76 FR 39405 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-06

... blood donors and its implications for selective testing of blood donors. On August 3, 2011, the...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). The meeting will be open to the public. Name of Committee: Blood Products Advisory...

Non-invasive spectroscopy of transfusable red blood cells stored inside sealed plastic blood-bags.

PubMed

Buckley, K; Atkins, C G; Chen, D; Schulze, H G; Devine, D V; Blades, M W; Turner, R F B

2016-03-07

After being separated from (donated) whole blood, red blood cells are suspended in specially formulated additive solutions and stored (at 4 °C) in polyvinyl chloride (PVC) blood-bags until they are needed for transfusion. With time, the prepared red cell concentrate (RCC) is known to undergo biochemical changes that lower effectiveness of the transfusion, and thus regulations are in place that limit the storage period to 42 days. At present, RCC is not subjected to analytical testing prior to transfusion. In this study, we use Spatially Offset Raman Spectroscopy (SORS) to probe, non-invasively, the biochemistry of RCC inside sealed blood-bags. The retrieved spectra compare well with conventional Raman spectra (of sampled aliquots) and are dominated by features associated with hemoglobin. In addition to the analytical demonstration that SORS can be used to retrieve RCC spectra from standard clinical blood-bags without breaking the sterility of the system, the data reveal interesting detail about the oxygenation-state of the stored cells themselves, namely that some blood-bags unexpectedly contain measurable amounts of deoxygenated hemoglobin after weeks of storage. The demonstration that chemical information can be obtained non-invasively using spectroscopy will enable new studies of RCC degeneration, and points the way to a Raman-based instrument for quality-control in a blood-bank or hospital setting.

Increased blood product use among coronary artery bypass patients prescribed preoperative aspirin and clopidogrel

PubMed Central

Ray, Joel G; Deniz, Stacy; Olivieri, Anthony; Pollex, Erika; Vermeulen, Marian J; Alexander, Kurian S; Cain, David J; Cybulsky, Irene; Hamielec, Cindy M

2003-01-01

Background The administration of antiplatelet drugs before coronary artery bypass graft surgery (CABG) is associated with an increased risk of major hemorrhage and related surgical reexploration. Little is known about the relative effect of combined clopidogrel and aspirin on blood product use around the time of CABG. We evaluated the associated risk between the combined use of aspirin and clopidogrel and the transfusion of blood products perioperatively. Methods We retrospectively studied a cohort of 659 individuals who underwent a first CABG, without concomitant valvular or aortic surgery, at a single large Canadian cardiac surgical centre between January 2000 and April 2002. The four study exposure groups were those prescribed aspirin (n = 105), clopidogrel (n = 11), the combination of both (n = 46), or neither drug (n = 497), within 7 days prior to CABG. The primary study outcome was the excessive transfusion of blood products during CABG and up to the second post-operative day, defined as ≥ 2 units of packed red blood cells (PRBC), ≥ 2 units of fresh frozen plasma, ≥ 5 units of cryoprecipitate or ≥ 5 units of platelets. Secondary outcomes included the mean number of transfused units of each type of blood product. Results A greater mean number of units of PRBC were transfused among those who received clopidogrel alone (2.9) or in combination with aspirin (2.4), compared to those on aspirin alone (1.9) or neither antiplatelet drug (1.4) (P = 0.001). A similar trend was seen for the respective mean number of transfused units of platelets (3.6, 3.7, 1.3 and 1.0; P < 0.001) and fresh frozen plasma (2.5, 3.1, 2.3, 1.6; P = 0.01). Compared to non-users, the associated risk of excessive blood product transfusion was highest among recipients of aspirin and clopidogrel together (adjusted OR 2.2, 95% CI 1.1–4.3). No significant association was seen among lone users of aspirin (adjusted OR 1.0, 95% CI 0.6–1.6) or clopidogrel (adjusted OR 0.7, 95% CI 0.2–2

Non-coding RNAs: new biomarkers and therapeutic targets for esophageal cancer

PubMed Central

Ren, Zhipeng; Zhang, Guoliang

2017-01-01

Esophageal cancer is one of the most common gastrointestinal malignant diseases and there is still no effective treatment. The incidence of esophageal cancer in the world is relatively high and on the increase year by year. Thus, the elaboration on the carcinogenesis of esophageal cancer and the identification of new biomarkers and therapeutic targets is quite beneficial to optimizing the current therapeutic regimen for treating such deadly disease. More and more evidence has shown that non-coding RNAs play an important role in the development and progression of multiple human cancers, including esophageal cancer. microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two functional kinds of non-coding RNAs that have been well investigated. They exert tumor suppressive or promoting effect by specifically regulating the expression of certain downstream target genes, which is tumor specific. It is also proved that miRNAs and lncRNAs level in tissue and plasma from esophageal cancer patients are closely correlated with the survival and disease progression, which could be used as a prognostic factor and therapeutic target for esophageal cancer. PMID:28388588

Non-coding RNAs: new biomarkers and therapeutic targets for esophageal cancer.

PubMed

Hou, Xiaobin; Wen, Jiaxin; Ren, Zhipeng; Zhang, Guoliang

2017-06-27

Esophageal cancer is one of the most common gastrointestinal malignant diseases and there is still no effective treatment. The incidence of esophageal cancer in the world is relatively high and on the increase year by year. Thus, the elaboration on the carcinogenesis of esophageal cancer and the identification of new biomarkers and therapeutic targets is quite beneficial to optimizing the current therapeutic regimen for treating such deadly disease. More and more evidence has shown that non-coding RNAs play an important role in the development and progression of multiple human cancers, including esophageal cancer. microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two functional kinds of non-coding RNAs that have been well investigated. They exert tumor suppressive or promoting effect by specifically regulating the expression of certain downstream target genes, which is tumor specific. It is also proved that miRNAs and lncRNAs level in tissue and plasma from esophageal cancer patients are closely correlated with the survival and disease progression, which could be used as a prognostic factor and therapeutic target for esophageal cancer.

Performance of the dot product function in radiative transfer code SORD

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-10-01

The successive orders of scattering radiative transfer (RT) codes frequently call the scalar (dot) product function. In this paper, we study performance of some implementations of the dot product in the RT code SORD using 50 scenarios for light scattering in the atmosphere-surface system. In the dot product function, we use the unrolled loops technique with different unrolling factor. We also considered the intrinsic Fortran functions. We show results for two machines: ifort compiler under Windows, and pgf90 under Linux. Intrinsic DOT_PRODUCT function showed best performance for the ifort. For the pgf90, the dot product implemented with unrolling factor 4 was the fastest. The RT code SORD together with the interface that runs all the mentioned tests are publicly available from ftp://maiac.gsfc.nasa.gov/pub/skorkin/SORD_IP_16B (current release) or by email request from the corresponding (first) author.

Colour coding for blood collection tube closures - a call for harmonisation.

PubMed

Simundic, Ana-Maria; Cornes, Michael P; Grankvist, Kjell; Lippi, Giuseppe; Nybo, Mads; Ceriotti, Ferruccio; Theodorsson, Elvar; Panteghini, Mauro

2015-02-01

At least one in 10 patients experience adverse events while receiving hospital care. Many of the errors are related to laboratory diagnostics. Efforts to reduce laboratory errors over recent decades have primarily focused on the measurement process while pre- and post-analytical errors including errors in sampling, reporting and decision-making have received much less attention. Proper sampling and additives to the samples are essential. Tubes and additives are identified not only in writing on the tubes but also by the colour of the tube closures. Unfortunately these colours have not been standardised, running the risk of error when tubes from one manufacturer are replaced by the tubes from another manufacturer that use different colour coding. EFLM therefore supports the worldwide harmonisation of the colour coding for blood collection tube closures and labels in order to reduce the risk of pre-analytical errors and improve the patient safety.

Development of blood transfusion product pathogen reduction treatments: a review of methods, current applications and demands.

PubMed

Salunkhe, Vishal; van der Meer, Pieter F; de Korte, Dirk; Seghatchian, Jerard; Gutiérrez, Laura

2015-02-01

Transfusion-transmitted infections (TTI) have been greatly reduced in numbers due to the strict donor selection and screening procedures, i.e. the availability of technologies to test donors for endemic infections, and routine vigilance of regulatory authorities in every step of the blood supply chain (collection, processing and storage). However, safety improvement is still a matter of concern because infection zero-risk in transfusion medicine is non-existent. Alternatives are required to assure the safety of the transfusion product and to provide a substitution to systematic blood screening tests, especially in less-developed countries or at the war-field. Furthermore, the increasing mobility of the population due to traveling poses a new challenge in the endemic screening tests routinely used, because non-endemic pathogens might emerge in a specific population. Pathogen reduction treatments sum a plethora of active approaches to eliminate or reduce potential threatening pathogen load from blood transfusion products. Despite the success of pathogen reduction treatments applied to plasma products, there is still a long way to develop and deploy pathogen reduction treatments to cellular transfusion products (such as platelets, RBCs or even to whole blood) and there is divergence on its acceptance worldwide. While the use of pathogen reduction treatments in platelets is performed routinely in a fair number of European blood banks, most of these treatments are not (or just) licensed in the USA or elsewhere in the world. The development of pathogen reduction treatments for RBC and whole blood is still in its infancy and under clinical trials. In this review, we discuss the available and emerging pathogen reduction treatments and their advantages and disadvantages. Furthermore, we highlight the importance of characterizing standard transfusion products with current and emerging approaches (OMICS) and clinical outcome, and integrating this information on a database

Does the Holland Code Predict Job Satisfaction and Productivity in Clothing Factory Workers?

ERIC Educational Resources Information Center

Heesacker, Martin; And Others

1988-01-01

Administered Self-Directed Search to sewing machine operators to determine Holland code, and assessed work productivity, job satisfaction, absenteeism, and insurance claims. Most workers were of the Social code. Social subjects were the most satisfied, Conventional and Realistic subjects next, and subjects of other codes less so. Productivity of…

Python Radiative Transfer Emission code (PyRaTE): non-LTE spectral lines simulations

NASA Astrophysics Data System (ADS)

Tritsis, A.; Yorke, H.; Tassis, K.

2018-05-01

We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability method. When computing the escape probability, the optical depth is calculated towards all directions with density, molecular abundance, temperature and velocity variations all taken into account. A very easy-to-use interface, capable of importing data from simulations outputs performed with all major astrophysical codes, is also developed. The code is written in PYTHON using an "embarrassingly parallel" strategy and can handle all geometries and projection angles. We benchmark the code by comparing our results with those from RADEX (van der Tak et al. 2007) and against analytical solutions and present case studies using hydrochemical simulations. The code will be released for public use.

Annual Coded Wire Tag Program; Missing Production Groups, 1996 Annual Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pastor, Stephen M.

1997-01-01

In 1989 the Bonneville Power Administration (BPA) began funding the evaluation of production groups of juvenile anadromous fish not being coded-wire tagged for other programs. These groups were the ''Missing Production Groups''. Production fish released by the U.S. Fish and Wildlife Service (USFWS) without representative coded-wire tags during the 1980's are indicated as blank spaces on the survival graphs in this report. The objectives of the ''Missing Production Groups'' program are: (1) to estimate the total survival of each production group, (2) to estimate the contribution of each production group to various fisheries, and (3) to prepare an annual reportmore » for all USFWS hatcheries in the Columbia River basin. Coded-wire tag recovery information will be used to evaluate the relative success of individual brood stocks. This information can also be used by salmon harvest managers to develop plans to allow the harvest of excess hatchery fish while protecting threatened, endangered, or other stocks of concern. In order to meet these objectives, a minimum of one marked group of fish is necessary for each production release. The level of marking varies according to location, species, and age at release. In general, 50,000 fish are marked with a coded-wire tag (CWT) to represent each production release group at hatcheries below John Day Dam. More than 100,000 fish per group are usually marked at hatcheries above John Day Dam. All fish release information, including marked/unmarked ratios, is reported to the Pacific States Marine Fisheries Commission (PSMFC). Fish recovered in the various fisheries or at the hatcheries are sampled to recover coded-wire tags. This recovery information is also reported to PSMFC.« less

Product code optimization for determinate state LDPC decoding in robust image transmission.

PubMed

Thomos, Nikolaos; Boulgouris, Nikolaos V; Strintzis, Michael G

2006-08-01

We propose a novel scheme for error-resilient image transmission. The proposed scheme employs a product coder consisting of low-density parity check (LDPC) codes and Reed-Solomon codes in order to deal effectively with bit errors. The efficiency of the proposed scheme is based on the exploitation of determinate symbols in Tanner graph decoding of LDPC codes and a novel product code optimization technique based on error estimation. Experimental evaluation demonstrates the superiority of the proposed system in comparison to recent state-of-the-art techniques for image transmission.

The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis.

PubMed

Ferreira, Flávia Viana; Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; de Oliveira, Karla Pollyanna Vieira; Silva, Emanuele Guimarães; Sant'Anna, Maurício Roberto Viana; Gontijo, Nelder de Figueiredo; Kroon, Erna Geessien; Imler, Jean Luc; Marques, João Trindade

2018-06-01

Sandflies are well known vectors for Leishmania but also transmit a number of arthropod-borne viruses (arboviruses). Few studies have addressed the interaction between sandflies and arboviruses. RNA interference (RNAi) mechanisms utilize small non-coding RNAs to regulate different aspects of host-pathogen interactions. The small interfering RNA (siRNA) pathway is a broad antiviral mechanism in insects. In addition, at least in mosquitoes, another RNAi mechanism mediated by PIWI interacting RNAs (piRNAs) is activated by viral infection. Finally, endogenous microRNAs (miRNA) may also regulate host immune responses. Here, we analyzed the small non-coding RNA response to Vesicular stomatitis virus (VSV) infection in the sandfly Lutzoymia longipalpis. We detected abundant production of virus-derived siRNAs after VSV infection in adult sandflies. However, there was no production of virus-derived piRNAs and only mild changes in the expression of vector miRNAs in response to infection. We also observed abundant production of virus-derived siRNAs against two other viruses in Lutzomyia Lulo cells. Together, our results suggest that the siRNA but not the piRNA pathway mediates an antiviral response in sandflies. In agreement with this hypothesis, pre-treatment of cells with dsRNA against VSV was able to inhibit viral replication while knock-down of the central siRNA component, Argonaute-2, led to increased virus levels. Our work begins to elucidate the role of RNAi mechanisms in the interaction between L. longipalpis and viruses and should also open the way for studies with other sandfly-borne pathogens.

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

PubMed

Ramsay, LeeAnn; Marchetto, Maria C; Caron, Maxime; Chen, Shu-Huang; Busche, Stephan; Kwan, Tony; Pastinen, Tomi; Gage, Fred H; Bourque, Guillaume

2017-02-28

A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs.

PubMed

Zucchelli, Silvia; Patrucco, Laura; Persichetti, Francesca; Gustincich, Stefano; Cotella, Diego

2016-01-01

Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.

Multilevel Concatenated Block Modulation Codes for the Frequency Non-selective Rayleigh Fading Channel

NASA Technical Reports Server (NTRS)

Lin, Shu; Rhee, Dojun

1996-01-01

This paper is concerned with construction of multilevel concatenated block modulation codes using a multi-level concatenation scheme for the frequency non-selective Rayleigh fading channel. In the construction of multilevel concatenated modulation code, block modulation codes are used as the inner codes. Various types of codes (block or convolutional, binary or nonbinary) are being considered as the outer codes. In particular, we focus on the special case for which Reed-Solomon (RS) codes are used as the outer codes. For this special case, a systematic algebraic technique for constructing q-level concatenated block modulation codes is proposed. Codes have been constructed for certain specific values of q and compared with the single-level concatenated block modulation codes using the same inner codes. A multilevel closest coset decoding scheme for these codes is proposed.

Blood product transfusion and wastage rates in obstetric hemorrhage.

PubMed

Yazer, Mark H; Dunbar, Nancy M; Cohn, Claudia; Dillon, Jessica; Eldib, Howida; Jackson, Bryon; Kaufman, Richard; Murphy, Michael F; O'Brien, Kerry; Raval, Jay S; Seheult, Jansen; Staves, Julie; Waters, Jonathan H

2018-03-07

Bleeding emergencies can complicate pregnancies. Understanding the disposition of the products that are issued in this clinical setting can help inform inventory levels at hospitals where obstetric patients are seen. Patients who had an obstetric hemorrhage of any etiology between January 2013 and June 2017, and whose resuscitation began with uncrossmatched red blood cells (RBCs) or emergency-issued plasma or platelets (PLT), were included. The disposition of all blood products issued within 6 hours of the first uncrossmatched or emergency-issued product was documented, as was basic patient demographic information. In total, 301 women with an obstetric hemorrhage from seven academic institutions were identified. Their mean ± standard deviation age was 30.9 ± 6.1 years, 45.2% delivered by Cesarean section, and 40.5% delivered vaginally, while 12% did not deliver. The largest single etiology of hemorrhage was related to abnormal placentation. Of the 2280 issued RBC units, 55% were transfused, 43% were returned, and 2% were wasted. The rates of transfusion of the other blood products ranged from 58% for plasma units to 82% for cryoprecipitate. Seventeen percent of the issued cryoprecipitate units were wasted, the highest of any blood product. The rate of a patient receiving a transfusion when at least one blood product had been ordered ranged from 74% for PLTs to 91% for cryoprecipitate. Although the rates of receiving a transfusion of at least one blood product when one is ordered was high, many of the issued units were returned, especially for RBCs. © 2018 AABB.

21 CFR 607.21 - Times for establishment registration and blood product listing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Times for establishment registration and blood... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.21 Times for establishment registration and blood product listing. The owner or operator of an...

21 CFR 607.21 - Times for establishment registration and blood product listing.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Times for establishment registration and blood... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.21 Times for establishment registration and blood product listing. The owner or operator of an...

21 CFR 607.21 - Times for establishment registration and blood product listing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Times for establishment registration and blood... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.21 Times for establishment registration and blood product listing. The owner or operator of an...

21 CFR 607.21 - Times for establishment registration and blood product listing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Times for establishment registration and blood... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.21 Times for establishment registration and blood product listing. The owner or operator of an...

21 CFR 607.21 - Times for establishment registration and blood product listing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Times for establishment registration and blood... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.21 Times for establishment registration and blood product listing. The owner or operator of an...

NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids

PubMed Central

Revilla-López, Guillem; Torras, Juan; Curcó, David; Casanovas, Jordi; Calaza, M. Isabel; Zanuy, David; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Grodzinski, Piotr; Alemán, Carlos

2010-01-01

Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids –also called non-coded, non-canonical or non-standard– is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, α-tetrasubstituted α-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example. PMID:20455555

[Long non-coding RNAs in plants].

PubMed

Xiaoqing, Huang; Dandan, Li; Juan, Wu

2015-04-01

Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides in length, widely exist in organisms and function in a variety of biological processes. Currently, most of lncRNAs found in plants are transcribed by RNA polymerase Ⅱ and mediate gene expression through multiple mechanisms, such as target mimicry, transcription interference, histone methylation and DNA methylation, and play important roles in flowering, male sterility, nutrition metabolism, biotic and abiotic stress and other biological processes as regulators in plants. In this review, we summarize the databases, prediction methods, and possible functions of plant lncRNAs discovered in recent years.

Efficiency of International Classification of Diseases, Ninth Revision, Billing Code Searches to Identify Emergency Department Visits for Blood or Body Fluid Exposures through a Statewide Multicenter Database

PubMed Central

Rosen, Lisa M.; Liu, Tao; Merchant, Roland C.

2016-01-01

BACKGROUND Blood and body fluid exposures are frequently evaluated in emergency departments (EDs). However, efficient and effective methods for estimating their incidence are not yet established. OBJECTIVE Evaluate the efficiency and accuracy of estimating statewide ED visits for blood or body fluid exposures using International Classification of Diseases, Ninth Revision (ICD-9), code searches. DESIGN Secondary analysis of a database of ED visits for blood or body fluid exposure. SETTING EDs of 11 civilian hospitals throughout Rhode Island from January 1, 1995, through June 30, 2001. PATIENTS Patients presenting to the ED for possible blood or body fluid exposure were included, as determined by prespecified ICD-9 codes. METHODS Positive predictive values (PPVs) were estimated to determine the ability of 10 ICD-9 codes to distinguish ED visits for blood or body fluid exposure from ED visits that were not for blood or body fluid exposure. Recursive partitioning was used to identify an optimal subset of ICD-9 codes for this purpose. Random-effects logistic regression modeling was used to examine variations in ICD-9 coding practices and styles across hospitals. Cluster analysis was used to assess whether the choice of ICD-9 codes was similar across hospitals. RESULTS The PPV for the original 10 ICD-9 codes was 74.4% (95% confidence interval [CI], 73.2%–75.7%), whereas the recursive partitioning analysis identified a subset of 5 ICD-9 codes with a PPV of 89.9% (95% CI, 88.9%–90.8%) and a misclassification rate of 10.1%. The ability, efficiency, and use of the ICD-9 codes to distinguish types of ED visits varied across hospitals. CONCLUSIONS Although an accurate subset of ICD-9 codes could be identified, variations across hospitals related to hospital coding style, efficiency, and accuracy greatly affected estimates of the number of ED visits for blood or body fluid exposure. PMID:22561713

Blood pressure and blood lipid levels among vegetarian, semi-vegetarian, and non-vegetarian native Africans.

PubMed

Famodu, A A; Osilesi, O; Makinde, Y O; Osonuga, O A

1998-10-01

Several epidemiological studies have implicated hypercholesterolemia and hypertriglyceridaemia as a dietary risk factor in the etiology of vascular disease. To date, there are virtually no blood lipid data available for Negroid Black African Seventh-Day Adventist vegetarians. This study was undertaken to gain a preliminary and better understanding of the relationships between BP, blood lipids, and diets in adults at the Seventh-Day Adventist Seminary of West Africa, Ilisan-Remo, Nigeria. Three randomly selected groups of the Nigerian populace with different dietary habits were investigated. The Seventh-Day Adventist Seminary of West Africa was the study area. Anthropometric measurements, blood pressure, serum cholesterol, triglycerides, and serum glucose were estimated using standard methods. The vegetarians (VEGs) had significantly lower body weight 75.0 +/- 1.9 kg than the semi-vegetarians (SEMI-VEGs) 77.3 +/- 1.8 kg (p < 0.05). There was no significant difference between the blood pressure (BP) of the three groups studied, although the VEGs exhibited lower systolic BP. The VEGs had significantly lower serum total cholesterol and triglycerides (p < 0.05), than non-vegetarians (NON-VEGs). The SEMI-VEGs had blood triglycerides values in between NON-VEGs and VEGs levels but these were not significant. There were no differences in blood glucose in the three groups. The vegetarian diet as well as the African natural diet are associated with lower levels of important cardiovascular disease risk factors. The significantly lower cardiovascular disease risk factors in vegetarian African Adventists could be a protective measure against the development of premature IHD and CVD incidence.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

PubMed

Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A; Dou, Dejing; Huang, Weili; Natale, Darren A; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T; Jiang, Guoqian; Lin, Yu; Wu, Bin; Strachan, Harrison J; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming

2016-01-01

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.

The role of the medical laboratory technologist in drinking and driving cases. Part 1: The Criminal Code and blood collection for alcohol analysis.

PubMed

Westenbrink, W

1992-01-01

Police officers can now demand blood samples from suspected impaired drivers in Canada to determine their Blood Alcohol Concentration. The medical laboratory technologist has been given the authority to take blood samples for legal purposes, as well as the authorization to complete certificates used as evidence in court. The proper procedures for the taking of blood samples and the completion of certificates are described in detail. The Criminal Code offences dealing with drinking and driving, the means by which police officers can legally obtain blood samples, the Blood Alcohol Kit, and the provision of providing blood collection evidence in court are discussed to aid the technologists in understanding their role in this process. The Criminal Code definitions of a "qualified medical practitioner", a "qualified technician", and "approved containers" are also described.

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR library

PubMed Central

Zhu, Shiyou; Li, Wei; Liu, Jingze; Chen, Chen-Hao; Liao, Qi; Xu, Ping; Xu, Han; Xiao, Tengfei; Cao, Zhongzheng; Peng, Jingyu; Yuan, Pengfei; Brown, Myles; Liu, Xiaole Shirley; Wei, Wensheng

2017-01-01

CRISPR/Cas9 screens have been widely adopted to analyse coding gene functions, but high throughput screening of non-coding elements using this method is more challenging, because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. Herein, we report a high throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We individually validated 9 lncRNAs using CRISPR/Cas9-mediated genomic deletion and functional rescue, CRISPR activation or inhibition, and gene expression profiling. Our high-throughput pgRNA genome deletion method should enable rapid identification of functional mammalian non-coding elements. PMID:27798563

75 FR 35494 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-22

... transfusions and the status of laboratory tests. On July 27, 2010, the committee will discuss blood donor...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). The meeting will be open to the public. Name of Committee: Blood Products Advisory...

Medical image classification based on multi-scale non-negative sparse coding.

PubMed

Zhang, Ruijie; Shen, Jian; Wei, Fushan; Li, Xiong; Sangaiah, Arun Kumar

2017-11-01

With the rapid development of modern medical imaging technology, medical image classification has become more and more important in medical diagnosis and clinical practice. Conventional medical image classification algorithms usually neglect the semantic gap problem between low-level features and high-level image semantic, which will largely degrade the classification performance. To solve this problem, we propose a multi-scale non-negative sparse coding based medical image classification algorithm. Firstly, Medical images are decomposed into multiple scale layers, thus diverse visual details can be extracted from different scale layers. Secondly, for each scale layer, the non-negative sparse coding model with fisher discriminative analysis is constructed to obtain the discriminative sparse representation of medical images. Then, the obtained multi-scale non-negative sparse coding features are combined to form a multi-scale feature histogram as the final representation for a medical image. Finally, SVM classifier is combined to conduct medical image classification. The experimental results demonstrate that our proposed algorithm can effectively utilize multi-scale and contextual spatial information of medical images, reduce the semantic gap in a large degree and improve medical image classification performance. Copyright © 2017 Elsevier B.V. All rights reserved.

21 CFR 607.25 - Information required for establishment registration and blood product listing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... registration and blood product listing. 607.25 Section 607.25 Food and Drugs FOOD AND DRUG ADMINISTRATION... FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.25 Information required for establishment registration and blood product listing. (a) Form...

21 CFR 607.25 - Information required for establishment registration and blood product listing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... registration and blood product listing. 607.25 Section 607.25 Food and Drugs FOOD AND DRUG ADMINISTRATION... FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.25 Information required for establishment registration and blood product listing. (a) Form...

21 CFR 607.25 - Information required for establishment registration and blood product listing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... registration and blood product listing. 607.25 Section 607.25 Food and Drugs FOOD AND DRUG ADMINISTRATION... FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.25 Information required for establishment registration and blood product listing. (a) Form...

Constacyclic codes over the ring F_q+v{F}_q+v2F_q and their applications of constructing new non-binary quantum codes

NASA Astrophysics Data System (ADS)

Ma, Fanghui; Gao, Jian; Fu, Fang-Wei

2018-06-01

Let R={F}_q+v{F}_q+v2{F}_q be a finite non-chain ring, where q is an odd prime power and v^3=v. In this paper, we propose two methods of constructing quantum codes from (α +β v+γ v2)-constacyclic codes over R. The first one is obtained via the Gray map and the Calderbank-Shor-Steane construction from Euclidean dual-containing (α +β v+γ v2)-constacyclic codes over R. The second one is obtained via the Gray map and the Hermitian construction from Hermitian dual-containing (α +β v+γ v2)-constacyclic codes over R. As an application, some new non-binary quantum codes are obtained.

Current Insights into Long Non-Coding RNAs in Renal Cell Carcinoma

PubMed Central

Seles, Maximilian; Hutterer, Georg C.; Kiesslich, Tobias; Pummer, Karl; Berindan-Neagoe, Ioana; Perakis, Samantha; Schwarzenbacher, Daniela; Stotz, Michael; Gerger, Armin; Pichler, Martin

2016-01-01

Renal cell carcinoma (RCC) represents a deadly disease with rising mortality despite intensive therapeutic efforts. It comprises several subtypes in terms of distinct histopathological features and different clinical presentations. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the genome which vary in expression levels and length and perform diverse functions. They are involved in the inititation, evolution and progression of primary cancer, as well as in the development and spread of metastases. Recently, several lncRNAs were described in RCC. This review emphasises the rising importance of lncRNAs in RCC. Moreover, it provides an outlook on their therapeutic potential in the future. PMID:27092491

Non-linear hydrodynamical evolution of rotating relativistic stars: numerical methods and code tests

NASA Astrophysics Data System (ADS)

Font, José A.; Stergioulas, Nikolaos; Kokkotas, Kostas D.

2000-04-01

We present numerical hydrodynamical evolutions of rapidly rotating relativistic stars, using an axisymmetric, non-linear relativistic hydrodynamics code. We use four different high-resolution shock-capturing (HRSC) finite-difference schemes (based on approximate Riemann solvers) and compare their accuracy in preserving uniformly rotating stationary initial configurations in long-term evolutions. Among these four schemes, we find that the third-order piecewise parabolic method scheme is superior in maintaining the initial rotation law in long-term evolutions, especially near the surface of the star. It is further shown that HRSC schemes are suitable for the evolution of perturbed neutron stars and for the accurate identification (via Fourier transforms) of normal modes of oscillation. This is demonstrated for radial and quadrupolar pulsations in the non-rotating limit, where we find good agreement with frequencies obtained with a linear perturbation code. The code can be used for studying small-amplitude or non-linear pulsations of differentially rotating neutron stars, while our present results serve as testbed computations for three-dimensional general-relativistic evolution codes.

A rational framework for production decision making in blood establishments.

PubMed

Ramoa, Augusto; Maia, Salomé; Lourenço, Anália

2012-07-24

SAD_BaSe is a blood bank data analysis software, created to assist in the management of blood donations and the blood production chain in blood establishments. In particular, the system keeps track of several collection and production indicators, enables the definition of collection and production strategies, and the measurement of quality indicators required by the Quality Management System regulating the general operation of blood establishments. This paper describes the general scenario of blood establishments and its main requirements in terms of data management and analysis. It presents the architecture of SAD_BaSe and identifies its main contributions. Specifically, it brings forward the generation of customized reports driven by decision making needs and the use of data mining techniques in the analysis of donor suspensions and donation discards.

A Rational Framework for Production Decision Making in Blood Establishments.

PubMed

Ramoa, Augusto; Maia, Salomé; Lourenço, Anália

2012-12-01

SAD_BaSe is a blood bank data analysis software, created to assist in the management of blood donations and the blood production chain in blood establishments. In particular, the system keeps track of several collection and production indicators, enables the definition of collection and production strategies, and the measurement of quality indicators required by the Quality Management System regulating the general operation of blood establishments. This paper describes the general scenario of blood establishments and its main requirements in terms of data management and analysis. It presents the architecture of SAD_BaSe and identifies its main contributions. Specifically, it brings forward the generation of customized reports driven by decision making needs and the use of data mining techniques in the analysis of donor suspensions and donation discards.

Tissue-Informative Mechanism for Wearable Non-invasive Continuous Blood Pressure Monitoring

NASA Astrophysics Data System (ADS)

Woo, Sung Hun; Choi, Yun Young; Kim, Dae Jung; Bien, Franklin; Kim, Jae Joon

2014-10-01

Accurate continuous direct measurement of the blood pressure is currently available thru direct invasive methods via intravascular needles, and is mostly limited to use during surgical procedures or in the intensive care unit (ICU). Non-invasive methods that are mostly based on auscultation or cuff oscillometric principles do provide relatively accurate measurement of blood pressure. However, they mostly involve physical inconveniences such as pressure or stress on the human body. Here, we introduce a new non-invasive mechanism of tissue-informative measurement, where an experimental phenomenon called subcutaneous tissue pressure equilibrium is revealed and related for application in detection of absolute blood pressure. A prototype was experimentally verified to provide an absolute blood pressure measurement by wearing a watch-type measurement module that does not cause any discomfort. This work is supposed to contribute remarkably to the advancement of continuous non-invasive mobile devices for 24-7 daily-life ambulatory blood-pressure monitoring.

The long non coding RNAs MHRT, FENDRR and CARMEN, their expression levels in peripheral blood mononuclear cells in patients with essential hypertension and their relation to heart hypertrophy.

PubMed

Kontaraki, Joanna E; Marketou, Maria E; Kochiadakis, George E; Maragkoudakis, Spyros; Konstantinou, John; Vardas, Panos E; Parthenakis, Fragiskos I

2018-06-19

Long non-coding RNAs (lncRNAs) participate in the modulation of cardiac hypertrophy and they represent potential therapeutic targets in cardiovascular disease. We investigated the expression profiles of selected lncRNAs in peripheral blood mononuclear cells of patients with essential hypertension in relation to left ventricular hypertrophy. We assessed the expression levels of the lncRNAs MHRT, FENDRR and CARMEN using real-time reverse transcription polymerase chain reaction. Hypertensive patients showed significantly higher MHRT, FENDRR and CARMEN expression levels compared with healthy controls. In addition, we observed significant negative correlations of MHRT (r=-0.323, p=0.003) and FENDRR (r=-0.380, p=0.001) and a positive correlation of CARMEN (r=0.458, p<0.001) expression levels with left ventricular mass index. Our data reveal that the lncRNAs MHRT, FENDRR and CARMEN show distinct expression profiles in hypertensive patients and they possibly represent candidate therapeutic targets in hypertensive heart disease. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Origin and evolution of the long non-coding genes in the X-inactivation center.

PubMed

Romito, Antonio; Rougeulle, Claire

2011-11-01

Random X chromosome inactivation (XCI), the eutherian mechanism of X-linked gene dosage compensation, is controlled by a cis-acting locus termed the X-inactivation center (Xic). One of the striking features that characterize the Xic landscape is the abundance of loci transcribing non-coding RNAs (ncRNAs), including Xist, the master regulator of the inactivation process. Recent comparative genomic analyses have depicted the evolutionary scenario behind the origin of the X-inactivation center, revealing that this locus evolved from a region harboring protein-coding genes. During mammalian radiation, this ancestral protein-coding region was disrupted in the marsupial group, whilst it provided in eutherian lineage the starting material for the non-translated RNAs of the X-inactivation center. The emergence of non-coding genes occurred by a dual mechanism involving loss of protein-coding function of the pre-existing genes and integration of different classes of mobile elements, some of which modeled the structure and sequence of the non-coding genes in a species-specific manner. The rising genes started to produce transcripts that acquired function in regulating the epigenetic status of the X chromosome, as shown for Xist, its antisense Tsix, Jpx, and recently suggested for Ftx. Thus, the appearance of the Xic, which occurred after the divergence between eutherians and marsupials, was the basis for the evolution of random X inactivation as a strategy to achieve dosage compensation. Copyright © 2011. Published by Elsevier Masson SAS.

Theory of epigenetic coding.

PubMed

Elder, D

1984-06-07

The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.

Accurate costs of blood transfusion: a microcosting of administering blood products in the United Kingdom National Health Service.

PubMed

Stokes, Elizabeth A; Wordsworth, Sarah; Staves, Julie; Mundy, Nicola; Skelly, Jane; Radford, Kelly; Stanworth, Simon J

2018-04-01

In an environment of limited health care resources, it is crucial for health care systems which provide blood transfusion to have accurate and comprehensive information on the costs of transfusion, incorporating not only the costs of blood products, but also their administration. Unfortunately, in many countries accurate costs for administering blood are not available. Our study aimed to generate comprehensive estimates of the costs of administering transfusions for the UK National Health Service. A detailed microcosting study was used to cost two key inputs into transfusion: transfusion laboratory and nursing inputs. For each input, data collection forms were developed to capture staff time, equipment, and consumables associated with each step in the transfusion process. Costing results were combined with costs of blood product wastage to calculate the cost per unit transfused, separately for different blood products. Data were collected in 2014/15 British pounds and converted to US dollars. A total of 438 data collection forms were completed by 74 staff. The cost of administering blood was $71 (£49) per unit for red blood cells, $84 (£58) for platelets, $55 (£38) for fresh-frozen plasma, and $72 (£49) for cryoprecipitate. Blood administration costs add substantially to the costs of the blood products themselves. These are frequently incurred costs; applying estimates to the blood components supplied to UK hospitals in 2015, the annual cost of blood administration, excluding blood products, exceeds $175 (£120) million. These results provide more accurate estimates of the total costs of transfusion than those previously available. © 2018 AABB.

21 CFR 607.20 - Who must register and submit a blood product list.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Who must register and submit a blood product list... BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.20 Who must register and submit a blood product list. (a) Owners or operators of all establishments, not exempt under...

21 CFR 607.20 - Who must register and submit a blood product list.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Who must register and submit a blood product list... BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.20 Who must register and submit a blood product list. (a) Owners or operators of all establishments, not exempt under...

21 CFR 607.20 - Who must register and submit a blood product list.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Who must register and submit a blood product list... BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.20 Who must register and submit a blood product list. (a) Owners or operators of all establishments, not exempt under...

21 CFR 607.20 - Who must register and submit a blood product list.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Who must register and submit a blood product list... BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.20 Who must register and submit a blood product list. (a) Owners or operators of all establishments, not exempt under...

21 CFR 607.20 - Who must register and submit a blood product list.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Who must register and submit a blood product list... BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.20 Who must register and submit a blood product list. (a) Owners or operators of all establishments, not exempt under...

Basic Business and Economics: Understanding the Uses of the Universal Product Code

ERIC Educational Resources Information Center

Blockhus, Wanda

1977-01-01

Describes the Universal Product Code (UPC), the two-part food labeling and packaging code which is both human- and electronic scanner-readable. Discusses how it affects both consumer and business, and suggests how to teach the UPC code to business education students. (HD)

A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear

PubMed Central

Corneveaux, Jason J.; Ohmen, Jeffrey; White, Cory; Allen, April N.; Lusis, Aldons J.; Van Camp, Guy; Huentelman, Matthew J.; Friedman, Rick A.

2015-01-01

The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https

Long non-coding RNA RUNXOR accelerates MDSC-mediated immunosuppression in lung cancer.

PubMed

Tian, Xinyu; Ma, Jie; Wang, Ting; Tian, Jie; Zheng, Yu; Peng, Rongrong; Wang, Yungang; Zhang, Yue; Mao, Lingxiang; Xu, Huaxi; Wang, Shengjun

2018-06-18

RUNX1 overlapping RNA (RUNXOR) is a long non-coding RNA that has been indicated as a key regulator in the development of myeloid cells by targeting runt-related transcription factor 1 (RUNX1). Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells consisting of immature granulocytes and monocytes with immunosuppression. However, the impact of lncRNA RUNXOR on the development of MDSCs remains unknown. Both the expressions of RUNXOR and RUNX1 in the peripheral blood were measured by qRT-PCR. Human MDSCs used in this study were isolated from tumor tissue of patients with lung cancer by FCM or induced from PBMCs of healthy donors with IL-1β + GM-CSF. Specific siRNA was used to knockdown the expression of RUNXOR in MDSCs. In this study, we found that the lncRNA RUNXOR was upregulated in the peripheral blood of lung cancer patients. In addition, as a target gene of RUNXOR, the expression of RUNX1 was downregulated in lung cancer patients. Finally, the expression of RUNXOR was higher in MDSCs isolated from the tumor tissues of lung cancer patients compared with cells from adjacent tissue. In addition, RUNXOR knockdown decreased Arg1 expression in MDSCs. Based on our findings, it is illustrated that RUNXOR is significantly associated with the immunosuppression induced by MDSCs in lung cancer patients and may be a target of anti-tumor therapy.

Strategies to reduce blood product utilization in obstetric practice.

PubMed

Neb, Holger; Zacharowski, Kai; Meybohm, Patrick

2017-06-01

Patient blood management (PBM) aims to improve patient outcome and safety by reducing the number of unnecessary RBC transfusions and vitalizing patient-specific anemia reserves. Although PBM is increasingly recognized as best clinical practice in elective surgery, implementation of PBM is restrained in the setting of obstetrics. This review summarizes recent findings to reduce blood product utilization in obstetric practice. PBM-related evidence-based benefits should be urgently adopted in the field of obstetric medicine. Intravenous iron can be considered a safe, effective strategy to replenish iron stores and to correct both pregnancy-related and hemorrhage-related iron deficiency anemia. In addition to surgical techniques and the use of uterotonics, recent findings support early administration of tranexamic acid, fibrinogen and a coagulation factor concentrate-based, viscoelastically guided practice in case of peripartum hemorrhage to manage coagulopathy. In patients with cesarean section, autologous red cell blood salvage may reduce blood product utilization, although its use in this setting is controversial. Implementation of PBM in obstetric practice offers large potential to reduce blood loss and transfusion requirements of allogeneic blood products, even though large clinical trials are lacking in this specific field. Intravenous iron supplementation may be suggested to increase peripartum hemoglobin levels. Additionally, tranexamic acid and point-of-care-guided supplementation of coagulation factors are potent methods to reduce unnecessary blood loss and blood transfusions in obstetrics.

Non-invasive determination of instantaneous brachial blood flow using the oscillometric method.

PubMed

Liu, Shing-Hong; Wang, Jia-Jung; Cheng, Da-Chuan

2009-08-01

The oscillometric method has been widely used to measure arterial systolic and diastolic blood pressures, but its potential for arterial blood flow measurements still remains to be explored. The aim of this study was to non-invasively determine arterial blood flow using an oscillometric blood flow measurement system. The system consists of a pneumatic elastic cuff, an air-pumping motor, a releaser valve, a pressure transducer, and an airflow meter. To build a non-linear cuff model, we measured airflow pumped into the pneumatic cuff and cuff pressure using an airflow meter and pressure transducer during the inflation period, respectively. During the deflation period, only the pressure transducer was used to record cuff pressure. Based on the cuff model, the oscillometric blood flow waveform was obtained by integrating the oscillometric pressure waveform. We compared arterial blood flow derived from the maximum amplitude of the oscillometric blood flow waveform with Doppler-measured blood flow calculated with the diameters and blood velocities of the brachial arteries in 32 subjects who underwent diagnostic evaluations for peripheral arterial embolism. A linear correlation coefficient of r = 0.716 was found between the oscillometry- and Doppler-based blood flow measurements in the 32 subjects. These results suggest that blood flow passing through the brachial artery can be quantified non-invasively using the oscillometric approach after appropriate calibration.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

PubMed Central

Juul, Malene; Bertl, Johanna; Guo, Qianyun; Nielsen, Morten Muhlig; Świtnicki, Michał; Hornshøj, Henrik; Madsen, Tobias; Hobolth, Asger; Pedersen, Jakob Skou

2017-01-01

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5’UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance. DOI: http://dx.doi.org/10.7554/eLife.21778.001 PMID:28362259

Oral warfarin affects peripheral blood leukocyte IL-6 and TNFα production in rats.

PubMed

Popov, Aleksandra; Belij, Sandra; Subota, Vesna; Zolotarevski, Lidija; Mirkov, Ivana; Kataranovski, Dragan; Kataranovski, Milena

2013-01-01

Warfarin is a Vitamin K (VK) antagonist that affects Vitamin K-dependent (VKD) processes, including blood coagulation, as well as processes unrelated to hemostasis such as bone growth, calcification, and growth of some cell types. In addition, warfarin exerts influence on some non-VKD-related activities, including anti-tumor and immunomodulating activity. With respect to the latter, both immune stimulating and suppressive effects have been noted in different experimental systems. To explore the in vivo immunomodulatory potential of warfarin on one type of activity (i.e., cytokine production) in two different immune cell populations (i.e., mononuclear or polymorphonuclear cells), effects of subchronic oral warfarin intake in rats on pro-inflammatory cytokine (i.e., TNFα, IL-6) production by peripheral blood mononuclear and polymorphonuclear cells (granulocytes) was examined. Differential effects of warfarin intake on TNFα and IL-6 were noted, depending on the type of peripheral blood leukocytes and on the cytokine examined. Specifically, a lack of effect on TNFα and a priming of IL-6 production by mononuclear cells along with a decrease in TNFα and a lack of effect on IL-6 in polymorphonuclear cells were seen in warfarin-exposed hosts. The cell- and cytokine-dependent effects from subchronic oral warfarin intake on peripheral blood leukocytes demonstrated in this study could, possibly, differentially affect reactions mediated by these cells. Ultimately, the observed effects in rats might have implications for those humans who are on long-term/prolonged warfarin therapy.

Long non-coding RNAs in hepatocellular carcinoma: Potential roles and clinical implications

PubMed Central

Niu, Zhao-Shan; Niu, Xiao-Jun; Wang, Wen-Hong

2017-01-01

Long non-coding RNAs (lncRNAs) are a subgroup of non-coding RNA transcripts greater than 200 nucleotides in length with little or no protein-coding potential. Emerging evidence indicates that lncRNAs may play important regulatory roles in the pathogenesis and progression of human cancers, including hepatocellular carcinoma (HCC). Certain lncRNAs may be used as diagnostic or prognostic markers for HCC, a serious malignancy with increasing morbidity and high mortality rates worldwide. Therefore, elucidating the functional roles of lncRNAs in tumors can contribute to a better understanding of the molecular mechanisms of HCC and may help in developing novel therapeutic targets. In this review, we summarize the recent progress regarding the functional roles of lncRNAs in HCC and explore their clinical implications as diagnostic or prognostic biomarkers and molecular therapeutic targets for HCC. PMID:28932078

The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

The effect of retrograde autologous priming on intraoperative blood product transfusion in coronary artery bypass grafting.

PubMed

Nanjappa, A; Gill, J; Sadat, U; Colah, S; Abu-Omar, Y; Nair, S

2013-11-01

Retrograde autologous priming (RAP) of the cardiopulmonary bypass (CPB) circuit could reduce the degree of haemodilution associated with priming with acellular solutions. However, there is no strong evidence to prove that the practice of RAP reduced intraoperative packed red cell (PRC) or blood product transfusion. To evaluate the effect of RAP on intraoperative PRC usage in coronary artery bypass grafting (CABG). This study is a prospective, observational study on patients who underwent first-time, isolated CABG using CPB between April 2012 and July 2012. Two groups of patients were identified: 1. Non-RAP group (n=128) and 2. RAP group (n=73). The primary outcome for the study was the amount of PRC and blood product usage between the induction of anaesthesia and the cessation of CPB. Use of PRC and blood products in the operating room was comparable in both groups. Univariate logistic regression showed that RAP was not an independent predictor of PRC or blood product transfusion (p=0.43). Multivariate logistic regression showed that CPB time, preoperative haemoglobin (Hb) levels and creatinine clearance were independent predictors of blood product transfusion. Practising RAP with mean volumes of 300 ml does not necessarily reduce PRC and other blood product transfusion requirements during CABG. In our practice, RAP was performed, aiming at displacing CPB circuit prime volume with which the perfusionist felt comfortable and dictated by haemodynamic parameters prior to commencing CPB. We presume this is the case in many units around the world. This practice, in our opinion, is not enough to achieve the benefits of RAP, if any, in the form of a reduction of packed red cell transfusion requirements. The true advantages of RAP in cardiac surgery need to be studied in a prospective, randomized, controlled trial.

Non-polar lipids accumulate during storage of transfusion products and do not contribute to the onset of transfusion-related acute lung injury.

PubMed

Peters, A L; Vervaart, M A T; van Bruggen, R; de Korte, D; Nieuwland, R; Kulik, W; Vlaar, A P J

2017-01-01

The accumulation of non-polar lipids arachidonic acid, 5-hydroxyeicosatetraenoic acid (HETE), 12-HETE and 15-HETE during storage of transfusion products may play a role in the onset of transfusion-related acute lung injury (TRALI), a syndrome of respiratory distress after transfusion. We investigated non-polar lipid accumulation in red blood cells (RBCs) stored for 42 days, plasma stored for 7 days at either 4 or 20°C and platelet (PLT) transfusion products stored for 7 days. Furthermore, we investigated whether transfusion of RBCs with increased levels of non-polar lipids induces TRALI in a 'two-hit' human volunteer model. All products were produced following Dutch Blood Bank protocols and are according to European standards. Non-polar lipids were measured with high-performance liquid chromotography followed by mass spectrometry. All non-polar lipids increased in RBCs after 21 days of storage compared to baseline. The non-polar lipid concentration in plasma increased significantly, and the increase was even more pronounced in products stored at 20°C. In platelets, baseline levels of 5-HETE and 15-HETE were higher than in RBCs or plasma. However, the non-polar lipids did not change significantly during storage of PLT products. Infusion of RBCs with increased levels of non-polar lipids did not induce TRALI in LPS-primed human volunteers. We conclude that non-polar lipids accumulate in RBC and plasma transfusion products and that accumulation is temperature dependent. Accumulation of non-polar lipids does not appear to explain the onset of TRALI (Dutch Trial Register - NTR4455). © 2016 International Society of Blood Transfusion.

Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain.

PubMed

Leighton, Laura J; Bredy, Timothy W

2018-06-07

Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.

Australian experience with frozen blood products on military operations.

PubMed

Neuhaus, Susan J; Wishaw, Ken; Lelkens, Charles

2010-02-15

Historically, the Australian Defence Force (ADF) has sourced all its blood supplies from the Australian Red Cross Blood Service. Recent ADF operations in the Middle East have highlighted a need to rely on other nations' blood supply systems. In 2008, the ADF embedded a surgical and intensive care team into the Netherlands-led forward health facility at the Uruzgan Medical Centre at Tarin Kowt in Afghanistan. To date, three teams have provided 2-month rotations as part of the North Atlantic Treaty Organization International Security Assistance Force in Afghanistan. The Netherlands armed forces use a sophisticated system for supply of liquid and frozen blood products (frozen red cells, plasma and platelets). We review Australian experience with the Dutch system of supplying blood products for major trauma resuscitation in Afghanistan.

Long non-coding RNAs in B-cell malignancies: a comprehensive overview

PubMed Central

Taiana, Elisa; Neri, Antonino

2017-01-01

B-cell malignancies constitute a large part of hematological neoplasias. They represent a heterogeneous group of diseases, including Hodgkin's lymphoma, most non-Hodgkin's lymphomas (NHL), some leukemias and myelomas. B-cell malignancies reflect defined stages of normal B-cell differentiation and this represents the major basis for their classification. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nucleotides, for which many recent studies have demonstrated a function in regulating gene expression, cell biology and carcinogenesis. Deregulated expression levels of lncRNAs have been observed in various types of cancers including hematological malignancies. The involvement of lncRNAs in cancer initiation and progression and their attractive features both as biomarker and for therapeutic research are becoming increasingly evident. In this review, we summarize the recent literature to highlight the status of the knowledge of lncRNAs role in normal B-cell development and in the pathogenesis of B-cell tumors. PMID:28947998

Modulation of cardiac autonomic tone in non-hypotensive hypovolemia during blood donation.

PubMed

Yadav, Kavita; Singh, Akanksha; Jaryal, Ashok Kumar; Coshic, Poonam; Chatterjee, Kabita; Deepak, K K

2017-08-01

Non-hypotensive hypovolemia, observed during mild haemorrhage or blood donation leads to reflex readjustment of the cardiac autonomic tone. In the present study, the cardiac autonomic tone was quantified using heart rate and blood pressure variability during and after non-hypotensive hypovolemia of blood donation. 86 voluntary healthy male blood donors were recruited for the study (age 35 ± 9 years; weight 78 ± 12 kg; height 174 ± 6 cms). Continuous lead II ECG and beat-to-beat blood pressure was recorded before, during and after blood donation followed by offline time and frequency domain analysis of HRV and BPV. The overall heart rate variability (SDNN and total power) did not change during or after blood donation. However, there was a decrease in indices that represent the parasympathetic component (pNN50 %, SDSD and HF) while an increase was observed in sympathetic component (LF) along with an increase in sympathovagal balance (LF:HF ratio) during blood donation. These changes were sustained for the period immediately following blood donation. No fall of blood pressure was observed during the period of study. The blood pressure variability showed an increase in the SDNN, CoV and RMSSD time domain measures in the post donation period. These results suggest that mild hypovolemia produced by blood donation is non-hypotensive but is associated with significant changes in the autonomic tone. The increased blood pressure variability and heart rate changes that are seen only in the later part of donation period could be because of the progressive hypovolemia associated parasympathetic withdrawal and sympathetic activation that manifest during the course of blood donation.

21 CFR 607.22 - How and where to register establishments and list blood products.

Code of Federal Regulations, 2014 CFR

2014-04-01

... blood products. 607.22 Section 607.22 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.22 How and where to register establishments and list blood products. (a) The first registration of an...

21 CFR 607.22 - How and where to register establishments and list blood products.

Code of Federal Regulations, 2013 CFR

2013-04-01

... blood products. 607.22 Section 607.22 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.22 How and where to register establishments and list blood products. (a) The first registration of an...

21 CFR 607.22 - How and where to register establishments and list blood products.

Code of Federal Regulations, 2012 CFR

2012-04-01

... blood products. 607.22 Section 607.22 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH... MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS Procedures for Domestic Blood Product Establishments § 607.22 How and where to register establishments and list blood products. (a) The first registration of an...

Long non-coding RNAs as novel expression signatures modulate DNA damage and repair in cadmium toxicology

NASA Astrophysics Data System (ADS)

Zhou, Zhiheng; Liu, Haibai; Wang, Caixia; Lu, Qian; Huang, Qinhai; Zheng, Chanjiao; Lei, Yixiong

2015-10-01

Increasing evidence suggests that long non-coding RNAs (lncRNAs) are involved in a variety of physiological and pathophysiological processes. Our study was to investigate whether lncRNAs as novel expression signatures are able to modulate DNA damage and repair in cadmium(Cd) toxicity. There were aberrant expression profiles of lncRNAs in 35th Cd-induced cells as compared to untreated 16HBE cells. siRNA-mediated knockdown of ENST00000414355 inhibited the growth of DNA-damaged cells and decreased the expressions of DNA-damage related genes (ATM, ATR and ATRIP), while increased the expressions of DNA-repair related genes (DDB1, DDB2, OGG1, ERCC1, MSH2, RAD50, XRCC1 and BARD1). Cadmium increased ENST00000414355 expression in the lung of Cd-exposed rats in a dose-dependent manner. A significant positive correlation was observed between blood ENST00000414355 expression and urinary/blood Cd concentrations, and there were significant correlations of lncRNA-ENST00000414355 expression with the expressions of target genes in the lung of Cd-exposed rats and the blood of Cd exposed workers. These results indicate that some lncRNAs are aberrantly expressed in Cd-treated 16HBE cells. lncRNA-ENST00000414355 may serve as a signature for DNA damage and repair related to the epigenetic mechanisms underlying the cadmium toxicity and become a novel biomarker of cadmium toxicity.

Frozen blood products: clinically effective and potentially ideal for remote Australia.

PubMed

Holley, A; Marks, D C; Johnson, L; Reade, M C; Badloe, J F; Noorman, F

2013-01-01

The development of effective cryopreservation techniques for both red blood cells and platelets, which maintain ex vivo biological activity, in combination with frozen plasma, provides for a unique blood banking strategy. This technology greatly enhances the storage life of these products. The rationale and potential advantages of using cryopreservation techniques for the provision of blood products to remote and military environments have been effectively demonstrated in several conflicts over the last decade. Current haemostatic resuscitation doctrine for the exsanguinating patient supports the use of red blood cells, platelets and frozen plasma early in the resuscitation. We believe an integrated fresh-frozen blood bank inventory could facilitate provision of blood products, not only in the military setting but also in regional Australia, by overcoming many logistic and geographical challenges. The processes involved in production and point of care thawing are sufficiently well developed and achievable to make this technology a viable option. The potential limitations of cryopreservation and subsequent product thawing need to be considered if such a strategy is to be developed. A substantial body of international experience using cryopreserved products in remote settings has already been accrued. This experience provides a template for the possible creation of an Australian integrated fresh-frozen blood bank inventory that could conceivably enhance the care of patients in both regional Australia and in the military setting.

Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

PubMed Central

Ashouri, Arghavan; Sayin, Volkan I.; Van den Eynden, Jimmy; Singh, Simranjit X.; Papagiannakopoulos, Thales; Larsson, Erik

2016-01-01

Thousands of long non-coding RNAs (lncRNAs) lie interspersed with coding genes across the genome, and a small subset has been implicated as downstream effectors in oncogenic pathways. Here we make use of transcriptome and exome sequencing data from thousands of tumours across 19 cancer types, to identify lncRNAs that are induced or repressed in relation to somatic mutations in key oncogenic driver genes. Our screen confirms known coding and non-coding effectors and also associates many new lncRNAs to relevant pathways. The associations are often highly reproducible across cancer types, and while many lncRNAs are co-expressed with their protein-coding hosts or neighbours, some are intergenic and independent. We highlight lncRNAs with possible functions downstream of the tumour suppressor TP53 and the master antioxidant transcription factor NFE2L2. Our study provides a comprehensive overview of lncRNA transcriptional alterations in relation to key driver mutational events in human cancers. PMID:28959951

Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-Expressed Gene Modules

PubMed Central

Spangler, Jacob B.; Ficklin, Stephen P.; Luo, Feng; Freeling, Michael; Feltus, F. Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome. PMID:23024789

Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.

PubMed

Spangler, Jacob B; Ficklin, Stephen P; Luo, Feng; Freeling, Michael; Feltus, F Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.

In silico screening of the chicken genome for overlaps between genomic regions: microRNA genes, coding and non-coding transcriptional units, QTL, and genetic variations.

PubMed

Zorc, Minja; Kunej, Tanja

2016-05-01

MicroRNAs (miRNAs) are a class of non-coding RNAs involved in posttranscriptional regulation of target genes. Regulation requires complementarity between target mRNA and the mature miRNA seed region, responsible for their recognition and binding. It has been estimated that each miRNA targets approximately 200 genes, and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals. In our previous study, we collected polymorphisms within miRNA genes in chicken. In the present study, we identified miRNA-related genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery. Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases: miRNA SNiPer, Ensembl, miRBase, NCBI Blast, and QTLdb. Out of 740 known pre-miRNA genes, 263 (35.5 %) contain polymorphisms; among them, 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are gga-miR-6662, containing 23 single nucleotide polymorphisms (SNPs) within the pre-miRNA region, including five consecutive SNPs, and gga-miR-6688, containing ten polymorphisms including three consecutive polymorphisms. Several miRNA-related genomic hotspots have been revealed in chicken genome; polymorphic miRNA genes are located within protein-coding and/or non-coding transcription units and quantitative trait loci (QTL) associated with production traits. The present study includes the first description of an exonic miRNA in a chicken genome, an overlap between the miRNA gene and the exon of the protein-coding gene (gga-miR-6578/HADHB), and the first report of a missense polymorphism located within a mature miRNA seed region. Identified miRNA-related genomic hotspots in chicken can serve researchers as a

Long non-coding RNA and Polycomb: an intricate partnership in cancer biology.

PubMed

Achour, Cyrinne; Aguilo, Francesca

2018-06-01

High-throughput analyses have revealed that the vast majority of the transcriptome does not code for proteins. These non-translated transcripts, when larger than 200 nucleotides, are termed long non-coding RNAs (lncRNAs), and play fundamental roles in diverse cellular processes. LncRNAs are subject to dynamic chemical modification, adding another layer of complexity to our understanding of the potential roles that lncRNAs play in health and disease. Many lncRNAs regulate transcriptional programs by influencing the epigenetic state through direct interactions with chromatin-modifying proteins. Among these proteins, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) have been shown to be recruited by lncRNAs to silence target genes. Aberrant expression, deficiency or mutation of both lncRNA and Polycomb have been associated with numerous human diseases, including cancer. In this review, we have highlighted recent findings regarding the concerted mechanism of action of Polycomb group proteins (PcG), acting together with some classically defined lncRNAs including X-inactive specific transcript ( XIST ), antisense non-coding RNA in the INK4 locus ( ANRIL ), metastasis associated lung adenocarcinoma transcript 1 ( MALAT1 ), and HOX transcript antisense RNA ( HOTAIR ).

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Erythroid cells in vitro: from developmental biology to blood transfusion products.

PubMed

Migliaccio, Anna Rita; Whitsett, Carolyn; Migliaccio, Giovanni

2009-07-01

Red blood cells (RBCs) transfusion plays a critical role in numerous therapies. Disruption of blood collection by political unrest, natural disasters and emerging infections and implementation of restrictions on the use of erythropoiesis-stimulating agents in cancer may impact blood availability in the near future. These considerations highlight the importance of developing alternative blood products. Knowledge about the processes that control RBC production has been applied to the establishment of culture conditions allowing ex-vivo generation of RBCs in numbers close to those (2.5 x 10 cells/ml) present in a transfusion, from cord blood, donated blood units or embryonic stem cells. In addition, experimental studies demonstrate that such cells protect mice from lethal bleeding. Therefore, erythroid cells generated ex vivo may be suitable for transfusion provided they can be produced safely in adequate numbers. However, much remains to be done to translate a theoretical production of approximately 2.5 x 10 RBCs in the laboratory into a 'clinical grade production process'. This review summarizes the state-of-the-art in establishing ex-vivo culture conditions for erythroid cells and discusses the most compelling issues to be addressed to translate this progress into a clinical grade transfusion product.

[Qualitative evaluation of blood products records in a hospital].

PubMed

Lartigue, B; Catillon, E

2012-02-01

This study aimed at evaluating the qualitative performance of blood products traceability from paper and electronic medical records in a hospital. Quality of date/time documentation was assessed by detection, for 20minutes or more, of chronological errors and inter-source inconsistencies, in a random sample of 168 blood products transfused during 2009. A receipt date/time was confirmed in 52% of paper records; a data entry error was attested in 25% of paper records, and 21% of electronic records. A transfusion date/time was notified in 93% of paper records, with a data entry error in 26% of paper records and 25% of electronic records. The patient medical record held at least one date/time error in 18% and 17%, for receipt and transfusion respectively. Environmental factors (clinical setting, urgency, blood product category) did not contributed to data error rates. Although blood products traceability has good quantitative results, the recorded documentation is not qualitative. In our study, data entry errors are similar in electronic or paper records, but the global failure rate is lesser in electronic records because omissions are controlled. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

The effects of non-Newtonian blood flow on curved stenotic coronary artery

NASA Astrophysics Data System (ADS)

Li, Shuang; Chin, Cheng; Monty, Jason; Barlis, Peter; Ooi, Andrew

2017-11-01

Direct numerical simulations (DNS) are carried out using both Newtonian and non-Newtonian viscosity models under a pulsatile physiological flow condition to study the influences of the non-Newtonian blood property on the flow fields in the idealised curved stenotic artery model. Quemada model is adopted to simulate the non-Newtonian blood in the simulations. Both time-averaged and selected instantaneous velocity, vorticity and pressure data are examined and the differences between the Newtonian and non-Newtonian flows are examined. The non-Newtonian simulations tend to have blunted axial velocity profile compared to the Newtonian cases. In the proximal of post-stenotic region, smaller recirculation bubbles are observed because of the non-Newtonian effects. Decreased secondary flow strengths are observed upstream of stenosis while higher magnitudes of secondary flows are found out downstream of stenosis. The deviation of mean cross-sectionally axial vorticity is minimal except at the peak systole, where an additional vortice appears near the centre of the 90 degrees plane that is more pronounced in the Newtonian case. The influence of blood-analog viscosity increases the mean pressure drops. However, lower instantaneous pressure losses at peak systole are observed in contrast to the Newtonian blood analog fluid.

78 FR 2677 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-14

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-N-0001] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). The meeting will be open to the public. Name of Committee: Blood Products Advisory...

The circulating non-coding RNA landscape for biomarker research: lessons and prospects from cardiovascular diseases.

PubMed

St Ecedil Pień, Ewa; Costa, Marina C; Kurc, Szczepan; Drożdż, Anna; Cortez-Dias, Nuno; Enguita, Francisco J

2018-06-07

Pervasive transcription of the human genome is responsible for the production of a myriad of non-coding RNA molecules (ncRNAs) some of them with regulatory functions. The pivotal role of ncRNAs in cardiovascular biology has been unveiled in the last decade, starting from the characterization of the involvement of micro-RNAs in cardiovascular development and function, and followed by the use of circulating ncRNAs as biomarkers of cardiovascular diseases. The human non-coding secretome is composed by several RNA species that circulate in body fluids and could be used as biomarkers for diagnosis and outcome prediction. In cardiovascular diseases, secreted ncRNAs have been described as biomarkers of several conditions including myocardial infarction, cardiac failure, and atrial fibrillation. Among circulating ncRNAs, micro-RNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been proposed as biomarkers in different cardiovascular diseases. In comparison with standard biomarkers, the biochemical nature of ncRNAs offers better stability and flexible storage conditions of the samples, and increased sensitivity and specificity. In this review we describe the current trends and future prospects of the use of the ncRNA secretome components as biomarkers of cardiovascular diseases, including the opening questions related with their secretion mechanisms and regulatory actions.

Benchmarking of neutron production of heavy-ion transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Long Non-coding RNAs in the X-inactivation Center

PubMed Central

Kalantry, Sundeep

2014-01-01

The X-inactivation center is a hotbed of functional long non-coding RNAs in eutherian mammals. These RNAs are thought to help orchestrate the epigenetic transcriptional states of the two X-chromosomes in females as well as of the single X-chromosome in males. To balance X-linked gene expression between the sexes, females undergo transcriptional silencing of most genes on one of the two X-chromosomes in a process termed X-chromosome inactivation. While one X-chromosome is inactivated, the other X-chromosome remains active. Moreover, with a few notable exceptions, the originally established epigenetic transcriptional profiles of the two is maintained as such through many rounds of cell division, essentially for the life of the organism. The stable divergent transcriptional fates of the two X-chromosomes, despite residing in a shared nucleoplasm, make X-inactivation a paradigm of epigenetic transcriptional regulation. Originally proposed in 1961 by Mary Lyon, the X-inactivation hypothesis has been validated through much experimentation over the last fifty years. In the last 25 years, the discovery and functional characterization has firmly established X-linked long non-coding RNAs as key players in choreographing X-chromosome inactivation. PMID:24297756

Parvovirus transmission by blood products - a cause for concern?

PubMed

Norja, Päivi; Lassila, Riitta; Makris, Mike

2012-11-01

The introduction of dual viral inactivation of clotting factor concentrates has practically eliminated infections by viruses associated with significant pathogenicity over the last 20 years. Despite this, theoretical concerns about transmission of infection have remained, as it is known that currently available viral inactivation methods are unable to eliminate parvovirus B19 or prions from these products. Recently, concern has been raised following the identification of the new parvoviruses, human parvovirus 4 (PARV4) and new genotypes of parvovirus B19, in blood products. Parvoviruses do not cause chronic pathogenicity similar to human immunodeficiency virus or hepatitis C virus, but nevertheless may cause clinical manifestations, especially in immunosuppressed patients. Manufacturers should institute measures, such as minipool polymerase chain reaction testing, to ensure that their products contain no known viruses. So far, human bocavirus, another new genus of parvovirus, has not been detected in fractionated blood products, and unless their presence can be demonstrated, routine testing during manufacture is not essential. Continued surveillance of the patients and of the safety of blood products remains an important ongoing issue. © 2012 Blackwell Publishing Ltd.

Suppressed cytokine production in whole blood cultures is related to iron status and is partially corrected following weight reduction in morbidly obese pre-menopausal women

USDA-ARS?s Scientific Manuscript database

Assess ex vivo whole-blood cytokine production and its association with iron status in obese versus non-obese women. Determine the change in ex vivo whole-blood cytokine production six months after restrictive bariatric surgery in the obese group. Subjects were 17 obese (BMI: 46.6 ±7.9 kg/m2) and 1...

Advanced GF(3²) nonbinary LDPC coded modulation with non-uniform 9-QAM outperforming star 8-QAM.

PubMed

Liu, Tao; Lin, Changyu; Djordjevic, Ivan B

2016-06-27

In this paper, we first describe a 9-symbol non-uniform signaling scheme based on Huffman code, in which different symbols are transmitted with different probabilities. By using the Huffman procedure, prefix code is designed to approach the optimal performance. Then, we introduce an algorithm to determine the optimal signal constellation sets for our proposed non-uniform scheme with the criterion of maximizing constellation figure of merit (CFM). The proposed nonuniform polarization multiplexed signaling 9-QAM scheme has the same spectral efficiency as the conventional 8-QAM. Additionally, we propose a specially designed GF(3²) nonbinary quasi-cyclic LDPC code for the coded modulation system based on the 9-QAM non-uniform scheme. Further, we study the efficiency of our proposed non-uniform 9-QAM, combined with nonbinary LDPC coding, and demonstrate by Monte Carlo simulation that the proposed GF(2³) nonbinary LDPC coded 9-QAM scheme outperforms nonbinary LDPC coded uniform 8-QAM by at least 0.8dB.

Functional Studies and In Silico Analyses to Evaluate Non-Coding Variants in Inherited Cardiomyopathies.

PubMed

Frisso, Giulia; Detta, Nicola; Coppola, Pamela; Mazzaccara, Cristina; Pricolo, Maria Rosaria; D'Onofrio, Antonio; Limongelli, Giuseppe; Calabrò, Raffaele; Salvatore, Francesco

2016-11-10

Point mutations are the most common cause of inherited diseases. Bioinformatics tools can help to predict the pathogenicity of mutations found during genetic screening, but they may work less well in determining the effect of point mutations in non-coding regions. In silico analysis of intronic variants can reveal their impact on the splicing process, but the consequence of a given substitution is generally not predictable. The aim of this study was to functionally test five intronic variants ( MYBPC3 -c.506-2A>C, MYBPC3 -c.906-7G>T, MYBPC3 -c.2308+3G>C, SCN5A -c.393-5C>A, and ACTC1 -c.617-7T>C) found in five patients affected by inherited cardiomyopathies in the attempt to verify their pathogenic role. Analysis of the MYBPC3 -c.506-2A>C mutation in mRNA from the peripheral blood of one of the patients affected by hypertrophic cardiac myopathy revealed the loss of the canonical splice site and the use of an alternative splicing site, which caused the loss of the first seven nucleotides of exon 5 ( MYBPC3 -G169AfsX14). In the other four patients, we generated minigene constructs and transfected them in HEK-293 cells. This minigene approach showed that MYBPC3 -c.2308+3G>C and SCN5A -c.393-5C>A altered pre-mRNA processing, thus resulting in the skipping of one exon. No alterations were found in either MYBPC3 -c.906-7G>T or ACTC1 -c.617-7T>C. In conclusion, functional in vitro analysis of the effects of potential splicing mutations can confirm or otherwise the putative pathogenicity of non-coding mutations, and thus help to guide the patient's clinical management and improve genetic counseling in affected families.

Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens

PubMed Central

Cho, Kyu Hong; Kim, Jeong-Ho

2015-01-01

Due to recent advances of bioinformatics and high throughput sequencing technology, discovery of regulatory non-coding RNAs in bacteria has been increased to a great extent. Based on this bandwagon, many studies searching for trans-acting small non-coding RNAs in streptococci have been performed intensively, especially in the important human pathogen, group A and B streptococci. However, studies for cis-encoded non-coding antisense RNAs in streptococci have been scarce. A recent study shows antisense RNAs are involved in virulence gene regulation in group B streptococcus, S. agalactiae. This suggests antisense RNAs could have important roles in the pathogenesis of streptococcal pathogens. In this review, we describe recent discoveries of chromosomal cis-encoded antisense RNAs in streptococcal pathogens and other low GC Gram (+) bacteria to provide a guide for future studies. PMID:25859258

Decoding the non-coding RNAs in Alzheimer's disease.

PubMed

Schonrock, Nicole; Götz, Jürgen

2012-11-01

Non-coding RNAs (ncRNAs) are integral components of biological networks with fundamental roles in regulating gene expression. They can integrate sequence information from the DNA code, epigenetic regulation and functions of multimeric protein complexes to potentially determine the epigenetic status and transcriptional network in any given cell. Humans potentially contain more ncRNAs than any other species, especially in the brain, where they may well play a significant role in human development and cognitive ability. This review discusses their emerging role in Alzheimer's disease (AD), a human pathological condition characterized by the progressive impairment of cognitive functions. We discuss the complexity of the ncRNA world and how this is reflected in the regulation of the amyloid precursor protein and Tau, two proteins with central functions in AD. By understanding this intricate regulatory network, there is hope for a better understanding of disease mechanisms and ultimately developing diagnostic and therapeutic tools.

Sampling methods to the statistical control of the production of blood components.

PubMed

Pereira, Paulo; Seghatchian, Jerard; Caldeira, Beatriz; Santos, Paula; Castro, Rosa; Fernandes, Teresa; Xavier, Sandra; de Sousa, Gracinda; de Almeida E Sousa, João Paulo

2017-12-01

The control of blood components specifications is a requirement generalized in Europe by the European Commission Directives and in the US by the AABB standards. The use of a statistical process control methodology is recommended in the related literature, including the EDQM guideline. The control reliability is dependent of the sampling. However, a correct sampling methodology seems not to be systematically applied. Commonly, the sampling is intended to comply uniquely with the 1% specification to the produced blood components. Nevertheless, on a purely statistical viewpoint, this model could be argued not to be related to a consistent sampling technique. This could be a severe limitation to detect abnormal patterns and to assure that the production has a non-significant probability of producing nonconforming components. This article discusses what is happening in blood establishments. Three statistical methodologies are proposed: simple random sampling, sampling based on the proportion of a finite population, and sampling based on the inspection level. The empirical results demonstrate that these models are practicable in blood establishments contributing to the robustness of sampling and related statistical process control decisions for the purpose they are suggested for. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modelling the effect of laminar axially directed blood flow on the dissolution of non-occlusive blood clots.

PubMed

Sersa, I; Vidmar, J; Grobelnik, B; Mikac, U; Tratar, G; Blinc, A

2007-06-07

Axially directed blood plasma flow can significantly accelerate thrombolysis of non-occlusive blood clots. Viscous forces caused by shearing of blood play an essential role in this process, in addition to biochemical fibrinolytic reactions. An analytical mathematical model based on the hypothesis that clot dissolution dynamics is proportional to the power of the flowing blood plasma dissipated along the clot is presented. The model assumes cylindrical non-occlusive blood clots with the flow channel in the centre, in which the flow is assumed to be laminar and flow rate constant at all times during dissolution. Effects of sudden constriction on the flow and its impact on the dissolution rate are also considered. The model was verified experimentally by dynamic magnetic resonance (MR) microscopy of artificial blood clots dissolving in an in vitro circulation system, containing plasma with a magnetic resonance imaging contrast agent and recombinant tissue-type plasminogen activator (rt-PA). Sequences of dynamically acquired 3D low resolution MR images of entire clots and 2D high resolution MR images of clots in the axial cross-section were used to evaluate the dissolution model by fitting it to the experimental data. The experimental data fitted well to the model and confirmed our hypothesis.

Iterative decoding of SOVA and LDPC product code for bit-patterned media recoding

NASA Astrophysics Data System (ADS)

Jeong, Seongkwon; Lee, Jaejin

2018-05-01

The demand for high-density storage systems has increased due to the exponential growth of data. Bit-patterned media recording (BPMR) is one of the promising technologies to achieve the density of 1Tbit/in2 and higher. To increase the areal density in BPMR, the spacing between islands needs to be reduced, yet this aggravates inter-symbol interference and inter-track interference and degrades the bit error rate performance. In this paper, we propose a decision feedback scheme using low-density parity check (LDPC) product code for BPMR. This scheme can improve the decoding performance using an iterative approach with extrinsic information and log-likelihood ratio value between iterative soft output Viterbi algorithm and LDPC product code. Simulation results show that the proposed LDPC product code can offer 1.8dB and 2.3dB gains over the one LDPC code at the density of 2.5 and 3 Tb/in2, respectively, when bit error rate is 10-6.

Long Non-Coding RNAs in Haematological Malignancies

PubMed Central

Garitano-Trojaola, Andoni; Agirre, Xabier; Prósper, Felipe; Fortes, Puri

2013-01-01

Long non-coding RNAs (lncRNAs) are functional RNAs longer than 200 nucleotides in length. LncRNAs are as diverse as mRNAs and they normally share the same biosynthetic machinery based on RNA polymerase II, splicing and polyadenylation. However, lncRNAs have low coding potential. Compared to mRNAs, lncRNAs are preferentially nuclear, more tissue specific and expressed at lower levels. Most of the lncRNAs described to date modulate the expression of specific genes by guiding chromatin remodelling factors; inducing chromosomal loopings; affecting transcription, splicing, translation or mRNA stability; or serving as scaffolds for the organization of cellular structures. They can function in cis, cotranscriptionally, or in trans, acting as decoys, scaffolds or guides. These functions seem essential to allow cell differentiation and growth. In fact, many lncRNAs have been shown to exert oncogenic or tumor suppressor properties in several cancers including haematological malignancies. In this review, we summarize what is known about lncRNAs, the mechanisms for their regulation in cancer and their role in leukemogenesis, lymphomagenesis and hematopoiesis. Furthermore, we discuss the potential of lncRNAs in diagnosis, prognosis and therapy in cancer, with special attention to haematological malignancies. PMID:23887658

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

DOE PAGES

Alam, Tanvir; Medvedeva, Yulia A.; Jia, Hui; ...

2014-10-02

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptionalmore » regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.« less

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alam, Tanvir; Medvedeva, Yulia A.; Jia, Hui

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptionalmore » regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.« less

Non-coding RNAs in virology: an RNA genomics approach.

PubMed

Isaac, Christopher; Patel, Trushar R; Zovoilis, Athanasios

2018-04-01

Advances in sequencing technologies and bioinformatic analysis techniques have greatly improved our understanding of various classes of RNAs and their functions. Despite not coding for proteins, non-coding RNAs (ncRNAs) are emerging as essential biomolecules fundamental for cellular functions and cell survival. Interestingly, ncRNAs produced by viruses not only control the expression of viral genes, but also influence host cell regulation and circumvent host innate immune response. Correspondingly, ncRNAs produced by the host genome can play a key role in host-virus interactions. In this article, we will first discuss a number of types of viral and mammalian ncRNAs associated with viral infections. Subsequently, we also describe the new possibilities and opportunities that RNA genomics and next-generation sequencing technologies provide for studying ncRNAs in virology.

Molecular interplay of pro-inflammatory transcription factors and non-coding RNAs in esophageal squamous cell carcinoma.

PubMed

Sundaram, Gopinath M; Veera Bramhachari, Pallaval

2017-06-01

Esophageal squamous cell carcinoma is the sixth most common cancer in the developing world. The aggressive nature of esophageal squamous cell carcinoma, its tendency for relapse, and the poor survival prospects of patients diagnosed at advanced stages, represent a pressing need for the development of new therapies for this disease. Chronic inflammation is known to have a causal link to cancer pre-disposition. Nuclear factor kappa B and signal transducer and activator of transcription 3 are transcription factors which regulate immunity and inflammation and are emerging as key regulators of tumor initiation, progression, and metastasis. Although these pro-inflammatory factors in esophageal squamous cell carcinoma have been well-characterized with reference to protein-coding targets, their functional interactions with non-coding RNAs have only recently been gaining attention. Non-coding RNAs, especially microRNAs and long non-coding RNAs demonstrate potential as biomarkers and alternative therapeutic targets. In this review, we summarize the recent literature and concepts on non-coding RNAs that are regulated by/regulate nuclear factor kappa B and signal transducer and activator of transcription 3 in esophageal cancer progression. We also discuss how these recent discoveries can pave way for future therapeutic options to treat esophageal squamous cell carcinoma.

Production Level CFD Code Acceleration for Hybrid Many-Core Architectures

NASA Technical Reports Server (NTRS)

Duffy, Austen C.; Hammond, Dana P.; Nielsen, Eric J.

2012-01-01

In this work, a novel graphics processing unit (GPU) distributed sharing model for hybrid many-core architectures is introduced and employed in the acceleration of a production-level computational fluid dynamics (CFD) code. The latest generation graphics hardware allows multiple processor cores to simultaneously share a single GPU through concurrent kernel execution. This feature has allowed the NASA FUN3D code to be accelerated in parallel with up to four processor cores sharing a single GPU. For codes to scale and fully use resources on these and the next generation machines, codes will need to employ some type of GPU sharing model, as presented in this work. Findings include the effects of GPU sharing on overall performance. A discussion of the inherent challenges that parallel unstructured CFD codes face in accelerator-based computing environments is included, with considerations for future generation architectures. This work was completed by the author in August 2010, and reflects the analysis and results of the time.

Long non-coding RNAs involved in autophagy regulation

PubMed Central

Yang, Lixian; Wang, Hanying; Shen, Qi; Feng, Lifeng; Jin, Hongchuan

2017-01-01

Autophagy degrades non-functioning or damaged proteins and organelles to maintain cellular homeostasis in a physiological or pathological context. Autophagy can be protective or detrimental, depending on its activation status and other conditions. Therefore, autophagy has a crucial role in a myriad of pathophysiological processes. From the perspective of autophagy-related (ATG) genes, the molecular dissection of autophagy process and the regulation of its level have been largely unraveled. However, the discovery of long non-coding RNAs (lncRNAs) provides a new paradigm of gene regulation in almost all important biological processes, including autophagy. In this review, we highlight recent advances in autophagy-associated lncRNAs and their specific autophagic targets, as well as their relevance to human diseases such as cancer, cardiovascular disease, diabetes and cerebral ischemic stroke. PMID:28981093

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term.

PubMed

Romero, Roberto; Tarca, Adi L; Chaemsaithong, Piya; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Jia, Hui; Hassan, Sonia S; Kalita, Cynthia A; Cai, Juan; Yeo, Lami; Lipovich, Leonard

2014-09-01

To identify differentially expressed long non-coding RNA (lncRNA) genes in human myometrium in women with spontaneous labor at term. Myometrium was obtained from women undergoing cesarean deliveries who were not in labor (n = 19) and women in spontaneous labor at term (n = 20). RNA was extracted and profiled using an Illumina® microarray platform. We have used computational approaches to bound the extent of long non-coding RNA representation on this platform, and to identify co-differentially expressed and correlated pairs of long non-coding RNA genes and protein-coding genes sharing the same genomic loci. We identified co-differential expression and correlation at two genomic loci that contain coding-lncRNA gene pairs: SOCS2-AK054607 and LMCD1-NR_024065 in women in spontaneous labor at term. This co-differential expression and correlation was validated by qRT-PCR, an experimental method completely independent of the microarray analysis. Intriguingly, one of the two lncRNA genes differentially expressed in term labor had a key genomic structure element, a splice site, that lacked evolutionary conservation beyond primates. We provide, for the first time, evidence for coordinated differential expression and correlation of cis-encoded antisense lncRNAs and protein-coding genes with known as well as novel roles in pregnancy in the myometrium of women in spontaneous labor at term.

BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.

PubMed

Ito, Eric Augusto; Katahira, Isaque; Vicente, Fábio Fernandes da Rocha; Pereira, Luiz Filipe Protasio; Lopes, Fabrício Martins

2018-06-05

With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and non-coding RNAs of 13 species and compared to the CNCI, PLEK and CPC2 methods. BASiNET outperformed all compared methods in all adopted organisms and datasets. BASiNET have classified sequences in all organisms with high accuracy and low standard deviation, showing that the method is robust and non-biased by the organism. The proposed methodology is implemented in open source in R language and freely available for download at https://cran.r-project.org/package=BASiNET.

Knowledge and practice of blood donation: a comparison between medical and non-medical Nepalese students.

PubMed

Mamatya, A; Prajapati, R; Yadav, R

2012-12-01

College students form a large and important group of population eligible for blood donation. Studies report that students do not donate much, and medical students' blood donation rate is less as compared to non-medical students. To assess and compare the knowledge, attitude, and practice of blood donation among medical and non-medical Nepalese students. A cross-sectional descriptive study using structured self-administered questionnaire was conducted in students of medical (MBBS) and non-medical programs of different colleges of Nepal. Total 456 students, 177 non-medical and 279 medical, participated; 28.5% students were donors. More medical students donated blood, more often, and were more knowledgeable in all aspects of blood and blood donation related knowledge (p values 0.01 or less). In both groups, proportionately more boys donated than girls. Common reasons for not donating included no request, medically unfit, no information about blood collection services, fear of weakness, and fear related to venepuncture. Moral satisfaction was the commonest reason to donate. Among Nepalese students, medical students donate more and are more knowledgeable than non-medical students. Lack of information and lack of direct requests are important causes of fewer donors in the non-medical group and girls.

Knowledge, attitudes and perceptions among non blood donor female health care professionals.

PubMed

Bilal, Muhammad; Haseeb, Abdul; Zahid, Ibrahim; Lashkerwala, Sehan Siraj; Saeeduddin, Fawad; Saad, Muhammad; Arshad, Mohammad Hussham; Moorpani, Manpreet; Khan, Midhat Zafar; Tariq, Ahsan; Habib, Haya; Islam, Tehrema; Advani, Rohan

2015-08-19

Blood donation is necessary in order to maintain an adequate supply of blood to patients who are suffering from any kind of disease or trauma, which requires them to have blood transfusion. Female non-blood donors are generally low in number. Therefore, this research was carried out to assess the main reasons behind the lack of blood donations made by females, and their knowledge, attitude and perceptions towards voluntary blood donation. A cross-sectional study was conducted on 664 female health professionals, who were selected by non-probability convenience sampling from two tertiary care hospitals. A pretested questionnaire was presented to the sample population, and the data was entered and analyzed on SPSS (V17). 94.6 % were aware with the fact that blood is screened for AIDS, Hepatitis B and C before transfusion. Moreover, 83.7% said that they will only donate blood if a family, relative or friend would need it and similarly 83.4%  suggested that they would donate blood if blood donation camps are arranged in hospital premises. 81.8 % thought that blood donors can contract Hepatitis B after donation where as only 29.5% did not blood due already blood loss in menstrual cycle. The participants had adequate knowledge about the benefits of blood donation. The most important reason identified for not donating blood is the lack of facilities within the workplace or lack of approach by responsible authorities. The results of the study may help in minimizing the misconceptions of the participants about blood transfusion, which would increase their contribution towards blood donation.

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

PubMed

Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

2017-10-03

Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes.

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes

PubMed Central

Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

2017-01-01

Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes. PMID:29108274

Plasma and Plasma Protein Product Transfusion: A Canadian Blood Services Centre for Innovation Symposium.

PubMed

Zeller, Michelle P; Al-Habsi, Khalid S; Golder, Mia; Walsh, Geraldine M; Sheffield, William P

2015-07-01

Plasma obtained via whole blood donation processing or via apheresis technology can either be transfused directly to patients or pooled and fractionated into plasma protein products that are concentrates of 1 or more purified plasma protein. The evidence base supporting clinical efficacy in most of the indications for which plasma is transfused is weak, whereas high-quality evidence supports the efficacy of plasma protein products in at least some of the clinical settings in which they are used. Transfusable plasma utilization remains composed in part of applications that fall outside of clinical practice guidelines. Plasma contains all of the soluble coagulation factors and is frequently transfused in efforts to restore or reinforce patient hemostasis. The biochemical complexities of coagulation have in recent years been rationalized in newer cell-based models that supplement the cascade hypothesis. Efforts to normalize widely used clinical hemostasis screening test values by plasma transfusion are thought to be misplaced, but superior rapid tests have been slow to emerge. The advent of non-vitamin K-dependent oral anticoagulants has brought new challenges to clinical laboratories in plasma testing and to clinicians needing to reverse non-vitamin K-dependent oral anticoagulants urgently. Current plasma-related controversies include prophylactic plasma transfusion before invasive procedures, plasma vs prothrombin complex concentrates for urgent warfarin reversal, and the utility of increased ratios of plasma to red blood cell units transfused in massive transfusion protocols. The first recombinant plasma protein products to reach the clinic were recombinant hemophilia treatment products, and these donor-free equivalents to factors VIII and IX are now being supplemented with novel products whose circulatory half-lives have been increased by chemical modification or genetic fusion. Achieving optimal plasma utilization is an ongoing challenge in the interconnected

Improvements to Busquet's Non LTE algorithm in NRL's Hydro code

NASA Astrophysics Data System (ADS)

Klapisch, M.; Colombant, D.

1996-11-01

Implementation of the Non LTE model RADIOM (M. Busquet, Phys. Fluids B, 5, 4191 (1993)) in NRL's RAD2D Hydro code in conservative form was reported previously(M. Klapisch et al., Bull. Am. Phys. Soc., 40, 1806 (1995)).While the results were satisfactory, the algorithm was slow and not always converging. We describe here modifications that address the latter two shortcomings. This method is quicker and more stable than the original. It also gives information about the validity of the fitting. It turns out that the number and distribution of groups in the multigroup diffusion opacity tables - a basis for the computation of radiation effects in the ionization balance in RADIOM- has a large influence on the robustness of the algorithm. These modifications give insight about the algorithm, and allow to check that the obtained average charge state is the true average. In addition, code optimization resulted in greatly reduced computing time: The ratio of Non LTE to LTE computing times being now between 1.5 and 2.

Fundamental study on non-invasive blood glucose sensing.

PubMed

Xu, K; Li, Q; Lu, Z; Jiang, J

2002-01-01

Diabetes is a disease which severely threatens the health of human beings. Unfortunately, current monitoring techniques with finger sticks discourage the regular use. Noninvasive spectroscopic measurement of blood glucose is a simple and painless technique, and reduces the long-term health care costs of diabetic patients due to no reagents. It is suitable for home use. Moreover, the establishment of the methodology not only applies to blood glucose noninvasive measurement, but also can be extended to noninvasive measurement of other analytes in body fluid, which will be of important significance for the development of the technique of clinical analysis. In this paper, some fundamental researches, which have been achieved in our laboratory in the field of non-invasive blood glucose measurement, were introduced. 1. Fundamental research was done for the glucose concentrations from simple to complex samples with near and middle infrared spectroscopy: (1) the relationship between the instrument precision and prediction accuracy of the glucose measurement; (2) the change of the result of the quantitative measurement with the change of the complexity of samples; (3) the attempt of increasing the prediction accuracy of the glucose measurement by improving the methods of modeling. The research results showed that it is feasible for non-invasive blood glucose measurement with near and middle infrared spectroscopy in theory, and the experimental results, from simple to complex samples, proved that it is effective for the methodology consisting of hardware and software. 2. According to the characteristics of human body measurement, the effects of measuring conditions on measurement results, such as: (1) the effect of measurement position; (2) the effect of measurement pressure; (3) the effect of measurement site; (4) the effect of measured individual, were investigated. With the fundamental researches, the special problems of human body measurement were solved. In addition

Comparison of Blood Lipids, Blood Pressures and Left Ventricular Cavity Dimension between Soccer Players and Non-Athletes

ERIC Educational Resources Information Center

Gokhan, Ismail; Kurkcu, Recep; Cekin, Resul

2013-01-01

In this study, it was aimed to compare the investigate the effects of regular exercise on blood lipids, blood pressure and left ventricular cavity dimensions function between soccer players and non-athletes in football players. This study consisted included a total of 30 subjects, including an experimental group including 18 soccer players…

An optical approach for non-invasive blood clot testing

NASA Astrophysics Data System (ADS)

Kalchenko, Vyacheslav; Brill, Alexander; Fine, Ilya; Harmelin, Alon

2007-02-01

Physiological blood coagulation is an essential biological process. Current tests for plasma coagulation (clotting) need to be performed ex vivo and require fresh blood sampling for every test. A recently published work describes a new, noninvasive, in vivo approach to assess blood coagulation status during mechanical occlusion1. For this purpose, we have tested this approach and applied a controlled laser beam to blood micro-vessels of the mouse ear during mechanical occlusion. Standard setup for intravital transillumination videomicroscopy and laser based imaging techniques were used for monitoring the blood clotting process. Temporal mechanical occlusion of blood vessels in the observed area was applied to ensure blood flow cessation. Subsequently, laser irradiation was used to induce vascular micro-injury. Changes in the vessel wall, as well as in the pattern of blood flow, predispose the area to vascular thrombosis, according to the paradigm of Virchow's triad. In our experiments, two elements of Virchow's triad were used to induce the process of clotting in vivo, and to assess it optically. We identified several parameters that can serve as markers of the blood clotting process in vivo. These include changes in light absorption in the area of illumination, as well as changes in the pattern of the red blood cells' micro-movement in the vessels where blood flow is completely arrested. Thus, our results indicate that blood coagulation status can be characterized by non-invasive, in vivo methodologies.

Present Scenario of Long Non-Coding RNAs in Plants

PubMed Central

Bhatia, Garima; Goyal, Neetu; Sharma, Shailesh; Upadhyay, Santosh Kumar; Singh, Kashmir

2017-01-01

Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in gene regulation, and their potent regulatory roles are being studied comprehensively in eukaryotes. LncRNAs were first reported in humans in 1992. Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. Additionally, numerous studies have been conducted to understand the roles of these long RNA species in several diseases. However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). Efforts are being made in this direction using computational tools and high-throughput sequencing technologies, such as the lncRNA microarray technique, RNA-sequencing (RNA-seq), RNA capture sequencing, (RNA CaptureSeq), etc. Given the current scenario, significant amounts of data have been produced regarding plant lncRNAs, and this amount is likely to increase in the subsequent years. In this review we have documented brief information about lncRNAs and their status of research in plants, along with the plant-specific resources/databases for information retrieval on lncRNAs. PMID:29657289

77 FR 29667 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-18

...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). At least one portion of the meeting will be closed to the public. Name of Committee: Blood... Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics...

78 FR 38351 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-26

...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). At least one portion of the meeting will be closed to the public. Name of Committee: Blood... Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics...

Non-coding RNAs, the Trojan horse in two-way communication between tumor and stroma in colorectal and hepatocellular carcinoma.

PubMed

Cătană, Cristina- Sorina; Pichler, Martin; Giannelli, Gianluigi; Mader, Robert M; Berindan-Neagoe, Ioana

2017-04-25

In a continuous and mutual exchange of information, cancer cells are invariably exposed to microenvironment transformation. This continuous alteration of the genetic, molecular and cellular peritumoral stroma background has become as critical as the management of primary tumor progression events in cancer cells. The communication between stroma and tumor cells within the extracellular matrix is one of the triggers in colon and liver carcinogenesis. All non- codingRNAs including long non-coding RNAs, microRNAs and ultraconserved genes play a critical role in almost all cancers and are responsible for the modulation of the tumor microenvironment in several malignant processes such as initiation, progression and dissemination. This review details the involvement of non codingRNAs in the evolution of human colorectal carcinoma and hepatocellular carcinoma in relationship with the microenvironment. Recent research has shown that a considerable number of dysregulated non- codingRNAs could be valuable diagnostic and prognostic biomarkers in cancer. Therefore, more in-depth knowledge of the role non- codingRNAs play in stroma-tumor communication and of the complex regulatory mechanisms between ultraconserved genes and microRNAs supports the validation of future effective therapeutic targets in patients suffering from hepatocellular and colorectal carcinoma, two distinctive entities which share quite a lot common non-coding RNAs.

Non-coding RNAs, the Trojan horse in two-way communication between tumor and stroma in colorectal and hepatocellular carcinoma

PubMed Central

Cătană, Cristina- Sorina; Pichler, Martin; Giannelli, Gianluigi; Mader, Robert M.; Berindan-Neagoe, Ioana

2017-01-01

In a continuous and mutual exchange of information, cancer cells are invariably exposed to microenvironment transformation. This continuous alteration of the genetic, molecular and cellular peritumoral stroma background has become as critical as the management of primary tumor progression events in cancer cells. The communication between stroma and tumor cells within the extracellular matrix is one of the triggers in colon and liver carcinogenesis. All non- codingRNAs including long non-coding RNAs, microRNAs and ultraconserved genes play a critical role in almost all cancers and are responsible for the modulation of the tumor microenvironment in several malignant processes such as initiation, progression and dissemination. This review details the involvement of non codingRNAs in the evolution of human colorectal carcinoma and hepatocellular carcinoma in relationship with the microenvironment. Recent research has shown that a considerable number of dysregulated non- codingRNAs could be valuable diagnostic and prognostic biomarkers in cancer. Therefore, more in-depth knowledge of the role non- codingRNAs play in stroma-tumor communication and of the complex regulatory mechanisms between ultraconserved genes and microRNAs supports the validation of future effective therapeutic targets in patients suffering from hepatocellular and colorectal carcinoma, two distinctive entities which share quite a lot common non-coding RNAs. PMID:28392501

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

PubMed Central

Kress, W. John; Erickson, David L.

2007-01-01

Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. PMID:17551588

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

PubMed

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

"ON ALGEBRAIC DECODING OF Q-ARY REED-MULLER AND PRODUCT REED-SOLOMON CODES"

DOE Office of Scientific and Technical Information (OSTI.GOV)

SANTHI, NANDAKISHORE

We consider a list decoding algorithm recently proposed by Pellikaan-Wu for q-ary Reed-Muller codes RM{sub q}({ell}, m, n) of length n {le} q{sup m} when {ell} {le} q. A simple and easily accessible correctness proof is given which shows that this algorithm achieves a relative error-correction radius of {tau} {le} (1-{radical}{ell}q{sup m-1}/n). This is an improvement over the proof using one-point Algebraic-Geometric decoding method given in. The described algorithm can be adapted to decode product Reed-Solomon codes. We then propose a new low complexity recursive aJgebraic decoding algorithm for product Reed-Solomon codes and Reed-Muller codes. This algorithm achieves a relativemore » error correction radius of {tau} {le} {Pi}{sub i=1}{sup m} (1 - {radical}k{sub i}/q). This algorithm is then proved to outperform the Pellikaan-Wu algorithm in both complexity and error correction radius over a wide range of code rates.« less

Improving appropriateness of blood utilization through prospective review of requests for blood products: the role of pathology residents as consultants.

PubMed

Haldiman, Lindsey; Zia, Hamid; Singh, Gurmukh

2014-01-01

To evaluate the effectiveness of prospective review of orders for fresh-frozen plasma (FFP) and platelets in reducing blood-product use, and of the effectiveness of preparing pathology residents to serve as clinical consultants. At our 572-bed tertiary-care hospital, we developed guidelines for the use of blood products in collaboration with a variety of departments. For patients whose condition(s) met generally accepted criteria, we identified trigger points to allow for quick release by blood bank staff of blood products. For patients whose condition(s) did not meet the applicable criteria, the on-call pathology resident reviewed the medical record of that patient to determine whether there were any extenuating circumstances; consulted with the ordering physician and attending pathologist, as needed; and advised the house staff on appropriate use of blood products. We evaluated the change in use of blood products between the years 2009 and 2012 to assess the effectiveness of the program. We observed a decrease of 38.8% and 31.4% in the use of FFP and platelets, respectively (29.7% and 21.1%, respectively, when normalized for the number of discharges). If projected to the national level, this improvement would translate to an annual cost reduction of approximately $130 million. Prospective review of orders for blood products can significantly improve use of these products, thereby reducing risk to patients and avoiding unnecessary healthcare costs. The involvement of pathology residents in the prospective review process provides an excellent opportunity for their training as laboratory consultants. Copyright© by the American Society for Clinical Pathology (ASCP).

Blood and Blood Product Conservation: Results of Strategies to Improve Clinical Outcomes in Open Heart Surgery Patients at a Tertiary Hospital.

PubMed

Khan, Junaid H; Green, Emily A; Chang, Jimmin; Ayala, Alexandria M; Barkin, Marilyn S; Reinys, Emily E; Stanton, Jeffrey; Stanten, Russell D

2017-12-01

Blood product usage is a quality outcome for patients undergoing cardiac surgery. To address an increase in blood product usage since the discontinuation of aprotinin, blood conservation strategies were initiated at a tertiary hospital in Oakland, CA. Improving transfusion rates for open heart surgery patients requiring Cardiopulmonary bypass (CPB) involved multiple departments in coordination. Specific changes to conserve blood product usage included advanced CPB technology upgrades, and precise individualized heparin dose response titration assay for heparin and protamine management. Retrospective analysis of blood product usage pre-implementation, post-CPB changes and post-Hemostasis Management System (HMS) implementation was done to determine the effectiveness of the blood conservation strategies. Statistically significant decrease in packed red blood cells, fresh frozen plasma, cryoprecipitate, and platelet usage over the stepped implementation of both technologies was observed. New oxygenator and centrifugal pump technologies reduced active circuitry volume and caused less damage to blood cells. Individualizing heparin and protamine dosing to a patient using the HMS led to transfusion reductions as well. Overall trends toward reductions in hospital length of stay and intensive care unit stay, and as a result, blood product cost and total hospitalization cost are positive over the period of implementation of both CPB circuit changes and HMS implementation. Although they are multifactorial in nature, these trends provide positive enforcement to the changes implemented.

Differences in social representation of blood donation between donors and non-donors: an empirical study.

PubMed

Guarnaccia, Cinzia; Giannone, Francesca; Falgares, Giorgio; Caligaris, Aldo Ozino; Sales-Wuillemin, Edith

2015-11-04

Both donors and non-donors have a positive image of blood donation, so donors and non-donors do not differ regarding their views on donation but do differ in converting their opinion into an active deed of donation. Several studies have identified altruism and empathy as the main factors underlying blood donation. However, a mixture of various motivational factors mould the complex behaviour of donation. This paper presents an exploratory study on differences of social representations of blood donation between blood donors and non-donors, in order to understand the reasons that bring someone to take the decision to become a blood donor. Participants filled in the Adapted Self-Report Altruism Scale, Toronto Empathy Questionnaire and answered a test of verbal association. Descriptive and correlation analyses were carried out on quantitative data, while a prototypic analysis was used for qualitative data. The study was carried out on a convenience sample of 786 individuals, 583 donors (mean age: 35.40 years, SD: 13.01 years; 39.3% female) and 203 non-donors (mean age: 35.10 years, SD: 13.30 years; 67.5% female). Social representations of donors seem to be more complex and articulated than those of non-donors. The terms that appear to be central were more specific in donors (life, needle, blood, help, altruism were the words most associated by non-donors; life, aid, altruism, solidarity, health, love, gift, generosity, voluntary, control, needed, useful, needle were the words most associated by donors). Furthermore, non-donors associated a larger number of terms referring to negative aspects of blood donation. Aspects related to training and the accuracy of any information on blood donation seem to be important in the decision to become a donor and stabilise the behaviour of donation over time, thus ensuring the highest levels of quality and safety in blood establishments.

Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

PubMed Central

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape. PMID:25540777

A method of non-contact reading code based on computer vision

NASA Astrophysics Data System (ADS)

Zhang, Chunsen; Zong, Xiaoyu; Guo, Bingxuan

2018-03-01

With the purpose of guarantee the computer information exchange security between internal and external network (trusted network and un-trusted network), A non-contact Reading code method based on machine vision has been proposed. Which is different from the existing network physical isolation method. By using the computer monitors, camera and other equipment. Deal with the information which will be on exchanged, Include image coding ,Generate the standard image , Display and get the actual image , Calculate homography matrix, Image distort correction and decoding in calibration, To achieve the computer information security, Non-contact, One-way transmission between the internal and external network , The effectiveness of the proposed method is verified by experiments on real computer text data, The speed of data transfer can be achieved 24kb/s. The experiment shows that this algorithm has the characteristics of high security, fast velocity and less loss of information. Which can meet the daily needs of the confidentiality department to update the data effectively and reliably, Solved the difficulty of computer information exchange between Secret network and non-secret network, With distinctive originality, practicability, and practical research value.

Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

PubMed

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

A Non Local Electron Heat Transport Model for Multi-Dimensional Fluid Codes

NASA Astrophysics Data System (ADS)

Schurtz, Guy

2000-10-01

Apparent inhibition of thermal heat flow is one of the most ancient problems in computational Inertial Fusion and flux-limited Spitzer-Harm conduction has been a mainstay in multi-dimensional hydrodynamic codes for more than 25 years. Theoretical investigation of the problem indicates that heat transport in laser produced plasmas has to be considered as a non local process. Various authors contributed to the non local theory and proposed convolution formulas designed for practical implementation in one-dimensional fluid codes. Though the theory, confirmed by kinetic calculations, actually predicts a reduced heat flux, it fails to explain the very small limiters required in two-dimensional simulations. Fokker-Planck simulations by Epperlein, Rickard and Bell [PRL 61, 2453 (1988)] demonstrated that non local effects could lead to a strong reduction of heat flow in two dimensions, even in situations where a one-dimensional analysis suggests that the heat flow is nearly classical. We developed at CEA/DAM a non local electron heat transport model suitable for implementation in our two-dimensional radiation hydrodynamic code FCI2. This model may be envisionned as the first step of an iterative solution of the Fokker-Planck equations; it takes the mathematical form of multigroup diffusion equations, the solution of which yields both the heat flux and the departure of the electron distribution function to the Maxwellian. Although direct implementation of the model is straightforward, formal solutions of it can be expressed in convolution form, exhibiting a three-dimensional tensor propagator. Reduction to one dimension retrieves the original formula of Luciani, Mora and Virmont [PRL 51, 1664 (1983)]. Intense magnetic fields may be generated by thermal effects in laser targets; these fields, as well as non local effects, will inhibit electron conduction. We present simulations where both effects are taken into account and shortly discuss the coupling strategy between them.

75 FR 12768 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-17

...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Administration (FDA). At least one portion of the meeting will be closed to the public. Name of Committee: Blood... Biochemistry and Vascular Biology, Division of Hematology, Office of Blood Research and Review, CBER, FDA. FDA...

77 FR 67013 - Blood Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-08

..., 2012, the Committee will meet in open session to discuss labeling of Red Blood Cells with historical...] Blood Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug Administration, HHS. ACTION... Food and Drug Administration (FDA). The meeting will be open to the public. Name of Committee: Blood...

TEG-Directed Transfusion in Complex Cardiac Surgery: Impact on Blood Product Usage.

PubMed

Fleming, Kevin; Redfern, Roberta E; March, Rebekah L; Bobulski, Nathan; Kuehne, Michael; Chen, John T; Moront, Michael

2017-12-01

Complex cardiac procedures often require blood transfusion because of surgical bleeding or coagulopathy. Thrombelastography (TEG) was introduced in our institution to direct transfusion management in cardiothoracic surgery. The goal of this study was to quantify the effect of TEG on transfusion rates peri- and postoperatively. All patients who underwent complex cardiac surgery, defined as open multiple valve repair/replacement, coronary artery bypass grafting with open valve repair/replacement, or aortic root/arch repair before and after implementation of TEG were identified and retrospectively analyzed. Minimally invasive cases were excluded. Patient characteristics and blood use were compared with t test and chi-square test. A generalized linear model including patient characteristics, preoperative and postoperative lab values, and autotransfusion volume was used to determine the impact of TEG on perioperative, postoperative, and total blood use. In total, 681 patients were identified, 370 in the pre-TEG period and 311 patients post-TEG. Patient demographics were not significantly different between periods. Mean units of red blood cells, plasma, and cryoprecipitate were significantly reduced after TEG was implemented (all, p < .0001); use of platelets was reduced but did not reach significance. Mean units of all blood products in the perioperative period and over the entire stay were reduced by approximately 40% (both, p < .0001). Total proportion of patients exposed to transfusion was significantly lower after introduction of TEG ( p < .01). Controlling for related factors on multivariate analysis, such as preoperative laboratory values and autotransfusion volume, use of TEG was associated with significant reduction in perioperative and overall blood product transfusion. TEG-directed management of blood product administration during complex cardiac surgeries significantly reduced the units of blood products received perioperatively but not blood usage more than

Drone transportation of blood products.

PubMed

Amukele, Timothy; Ness, Paul M; Tobian, Aaron A R; Boyd, Joan; Street, Jeff

2017-03-01

Small civilian unmanned aerial vehicles (drones) are a novel way to transport small goods. To the best of our knowledge there are no studies examining the impact of drone transport on blood products, describing approaches to maintaining temperature control, or component physical characteristics during drone transport. Six leukoreduced red blood cell (RBC) and six apheresis platelet (PLT) units were split using sterile techniques. The larger parent RBC and PLT units, as well as six unthawed plasma units frozen within 24 hours of collection (FP24), were placed in a cooler, attached to the drone, and flown for up to 26.5 minutes with temperature logging. Ambient temperatures during the experimental window ranged between -1 and 18°C across 2 days. The difference between the ambient and unit temperatures was approximately 20°C for PLT and FP24 units. After flight, the RBC parent units were centrifuged and visually checked for hemolysis; the PLTs were checked for changes in mean PLT volumes (MPVs), pH, and PLT count; and the frozen air bubbles on the back of the FP24 units were examined for any changes in size or shape, as evidence of thawing. There was no evidence of RBC hemolysis; no significant changes in PLT count, pH, or MPVs; and no changes in the FP24 bubbles. The temperature of all units was maintained during transport and flight. There was no adverse impact of drone transport on RBC, PLT, or FP24 units. These findings suggest that drone transportation systems are a viable option for the transportation of blood products. © 2016 AABB.

Non-Coding RNAs in Castration-Resistant Prostate Cancer: Regulation of Androgen Receptor Signaling and Cancer Metabolism.

PubMed

Shih, Jing-Wen; Wang, Ling-Yu; Hung, Chiu-Lien; Kung, Hsing-Jien; Hsieh, Chia-Ling

2015-12-04

Hormone-refractory prostate cancer frequently relapses from therapy and inevitably progresses to a bone-metastatic status with no cure. Understanding of the molecular mechanisms conferring resistance to androgen deprivation therapy has the potential to lead to the discovery of novel therapeutic targets for type of prostate cancer with poor prognosis. Progression to castration-resistant prostate cancer (CRPC) is characterized by aberrant androgen receptor (AR) expression and persistent AR signaling activity. Alterations in metabolic activity regulated by oncogenic pathways, such as c-Myc, were found to promote prostate cancer growth during the development of CRPC. Non-coding RNAs represent a diverse family of regulatory transcripts that drive tumorigenesis of prostate cancer and various other cancers by their hyperactivity or diminished function. A number of studies have examined differentially expressed non-coding RNAs in each stage of prostate cancer. Herein, we highlight the emerging impacts of microRNAs and long non-coding RNAs linked to reactivation of the AR signaling axis and reprogramming of the cellular metabolism in prostate cancer. The translational implications of non-coding RNA research for developing new biomarkers and therapeutic strategies for CRPC are also discussed.

Non-Coding RNAs in Castration-Resistant Prostate Cancer: Regulation of Androgen Receptor Signaling and Cancer Metabolism

PubMed Central

Shih, Jing-Wen; Wang, Ling-Yu; Hung, Chiu-Lien; Kung, Hsing-Jien; Hsieh, Chia-Ling

2015-01-01

Hormone-refractory prostate cancer frequently relapses from therapy and inevitably progresses to a bone-metastatic status with no cure. Understanding of the molecular mechanisms conferring resistance to androgen deprivation therapy has the potential to lead to the discovery of novel therapeutic targets for type of prostate cancer with poor prognosis. Progression to castration-resistant prostate cancer (CRPC) is characterized by aberrant androgen receptor (AR) expression and persistent AR signaling activity. Alterations in metabolic activity regulated by oncogenic pathways, such as c-Myc, were found to promote prostate cancer growth during the development of CRPC. Non-coding RNAs represent a diverse family of regulatory transcripts that drive tumorigenesis of prostate cancer and various other cancers by their hyperactivity or diminished function. A number of studies have examined differentially expressed non-coding RNAs in each stage of prostate cancer. Herein, we highlight the emerging impacts of microRNAs and long non-coding RNAs linked to reactivation of the AR signaling axis and reprogramming of the cellular metabolism in prostate cancer. The translational implications of non-coding RNA research for developing new biomarkers and therapeutic strategies for CRPC are also discussed. PMID:26690121

Non-coding RNAs—Novel targets in neurotoxicity

PubMed Central

Tal, Tamara L.; Tanguay, Robert L.

2012-01-01

Over the past ten years non-coding RNAs (ncRNAs) have emerged as pivotal players in fundamental physiological and cellular processes and have been increasingly implicated in cancer, immune disorders, and cardiovascular, neurodegenerative, and metabolic diseases. MicroRNAs (miRNAs) represent a class of ncRNA molecules that function as negative regulators of post-transcriptional gene expression. miRNAs are predicted to regulate 60% of all human protein-coding genes and as such, play key roles in cellular and developmental processes, human health, and disease. Relative to counterparts that lack bindings sites for miRNAs, genes encoding proteins that are post-transcriptionally regulated by miRNAs are twice as likely to be sensitive to environmental chemical exposure. Not surprisingly, miRNAs have been recognized as targets or effectors of nervous system, developmental, hepatic, and carcinogenic toxicants, and have been identified as putative regulators of phase I xenobiotic-metabolizing enzymes. In this review, we give an overview of the types of ncRNAs and highlight their roles in neurodevelopment, neurological disease, activity-dependent signaling, and drug metabolism. We then delve into specific examples that illustrate their importance as mediators, effectors, or adaptive agents of neurotoxicants or neuroactive pharmaceutical compounds. Finally, we identify a number of outstanding questions regarding ncRNAs and neurotoxicity. PMID:22394481

Identification and role of regulatory non-coding RNAs in Listeria monocytogenes.

PubMed

Izar, Benjamin; Mraheil, Mobarak Abu; Hain, Torsten

2011-01-01

Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- and trans-acting regulatory RNAs, including sRNAs, asRNAs, untranslated regions (UTR) and riboswitches. As a result, we obtained a more comprehensive view on the complexity and plasticity of the prokaryotic genome biology. Listeria monocytogenes was utilized as a model system for intracellular pathogenic bacteria in several studies, which revealed the presence of about 180 regulatory RNAs in the listerial genome. A regulatory role of non-coding RNAs in survival, virulence and adaptation mechanisms of L. monocytogenes was confirmed in subsequent experiments, thus, providing insight into a multifaceted modulatory function of RNA/mRNA interference. In this review, we discuss the identification of regulatory RNAs by high-throughput techniques and in their functional role in L. monocytogenes.

Chirp- and random-based coded ultrasonic excitation for localized blood-brain barrier opening

PubMed Central

Kamimura, HAS; Wang, S; Wu, S-Y; Karakatsani, ME; Acosta, C; Carneiro, AAO; Konofagou, EE

2015-01-01

Chirp- and random-based coded excitation methods have been proposed to reduce standing wave formation and improve focusing of transcranial ultrasound. However, no clear evidence has been shown to support the benefits of these ultrasonic excitation sequences in vivo. This study evaluates the chirp and periodic selection of random frequency (PSRF) coded-excitation methods for opening the blood-brain barrier (BBB) in mice. Three groups of mice (n=15) were injected with polydisperse microbubbles and sonicated in the caudate putamen using the chirp/PSRF coded (bandwidth: 1.5-1.9 MHz, peak negative pressure: 0.52 MPa, duration: 30 s) or standard ultrasound (frequency: 1.5 MHz, pressure: 0.52 MPa, burst duration: 20 ms, duration: 5 min) sequences. T1-weighted contrast-enhanced MRI scans were performed to quantitatively analyze focused ultrasound induced BBB opening. The mean opening volumes evaluated from the MRI were 9.38±5.71 mm3, 8.91±3.91 mm3 and 35.47 ± 5.10 mm3 for the chirp, random and regular sonications, respectively. The mean cavitation levels were 55.40±28.43 V.s, 63.87±29.97 V.s and 356.52±257.15 V.s for the chirp, random and regular sonications, respectively. The chirp and PSRF coded pulsing sequences improved the BBB opening localization by inducing lower cavitation levels and smaller opening volumes compared to results of the regular sonication technique. Larger bandwidths were associated with more focused targeting but were limited by the frequency response of the transducer, the skull attenuation and the microbubbles optimal frequency range. The coded methods could therefore facilitate highly localized drug delivery as well as benefit other transcranial ultrasound techniques that use higher pressure levels and higher precision to induce the necessary bioeffects in a brain region while avoiding damage to the surrounding healthy tissue. PMID:26394091

Analytical Performance Evaluation of Infopia Element™ Auto-coding Blood Glucose Monitoring System for Self-Monitoring of Blood Glucose.

PubMed

Park, Hae-Il; Lee, Seong-Su; Son, Jang-Won; Kwon, Hee-Sun; Kim, Sung Rae; Chae, Hyojin; Kim, Myungshin; Kim, Yonggoo; Yoo, Soonjib

2016-11-01

Element™ Auto-coding Blood Glucose Monitoring System (BGMS; Infopia Co., Ltd., Anyang-si, Korea) was developed for self-monitoring of blood glucose (SMBG). Precision, linearity, and interference were tested. Eighty-four capillary blood samples measured by Element™ BGMS were compared with central laboratory method (CLM) results in venous serum. Accuracy was evaluated using ISO 15197:2013 criteria. Coefficients of variation (CVs; mean) were 2.4% (44.2 mg/dl), 3.7% (100.6 mg/dl), and 2.1% (259.8 mg/dl). Linearity was shown at concentrations 39.25-456.25 mg/l (y = 0.989 + 0.984x, SE = 17.63). Up to 15 mg/dl of galactose, ascorbic acid, and acetaminophen, interference > 10.4% was not observed. Element™ BGMS glucose was higher than CLM levels by 3.2 mg/dl (at 200 mg/dl) to 8.2 mg/dl (at 100 mg/dl). The minimum specification for bias (3.3%) was met at 140 and 200 mg/l glucose. In the Clarke and consensus error grids, 100% of specimens were within zone A and B. For Element™ BGMS values, 92.9% (78/84) to 94.0% (79/84) were within a 15 mg/dl (< 100 mg/dl) or 15% (> 100 mg/dl) of the average CLM value. Element™ BGMS was considered an appropriate SMBG for home use; however, the positive bias at low-to-mid glucose levels requires further improvement. © 2016 Wiley Periodicals, Inc.

FPGA implementation of concatenated non-binary QC-LDPC codes for high-speed optical transport.

PubMed

Zou, Ding; Djordjevic, Ivan B

2015-06-01

In this paper, we propose a soft-decision-based FEC scheme that is the concatenation of a non-binary LDPC code and hard-decision FEC code. The proposed NB-LDPC + RS with overhead of 27.06% provides a superior NCG of 11.9dB at a post-FEC BER of 10^-15. As a result, the proposed NB-LDPC codes represent the strong FEC candidate of soft-decision FEC for beyond 100Gb/s optical transmission systems.

MicroRNAs and other non-coding RNAs as targets for anticancer drug development

PubMed Central

Ling, Hui; Fabbri, Muller; Calin, George A.

2015-01-01

With the first cancer-targeted microRNA drug, MRX34, a liposome-based miR-34 mimic, entering phase I clinical trial in patients with advanced hepatocellular carcinoma in April 2013, miRNA therapeutics are attracting special attention from both academia and biotechnology companies. Although to date the most studied non-coding RNAs (ncRNAs) are miRNAs, the importance of long non-coding RNAs (lncRNAs) is increasingly being recognized. Here we summarize the roles of miRNAs and lncRNAs in cancer, with a focus on the recently identified novel mechanisms of action, and discuss the current strategies in designing ncRNA-targeting therapeutics, as well as the associated challenges. PMID:24172333

Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury.

PubMed

Arthur-Farraj, Peter J; Morgan, Claire C; Adamowicz, Martyna; Gomez-Sanchez, Jose A; Fazal, Shaline V; Beucher, Anthony; Razzaghi, Bonnie; Mirsky, Rhona; Jessen, Kristjan R; Aitman, Timothy J

2017-09-12

Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

LncRNA-DANCR: A valuable cancer related long non-coding RNA for human cancers.

PubMed

Thin, Khaing Zar; Liu, Xuefang; Feng, Xiaobo; Raveendran, Sudheesh; Tu, Jian Cheng

2018-06-01

Long noncoding RNAs (lncRNA) are a type of noncoding RNA that comprise of longer than 200 nucleotides sequences. They can regulate chromosome structure, gene expression and play an essential role in the pathophysiology of human diseases, especially in tumorigenesis and progression. Nowadays, they are being targeted as potential biomarkers for various cancer types. And many research studies have proven that lncRNAs might bring a new era to cancer diagnosis and support treatment management. The purpose of this review was to inspect the molecular mechanism and clinical significance of long non-coding RNA- differentiation antagonizing nonprotein coding RNA(DANCR) in various types of human cancers. In this review, we summarize and figure out recent research studies concerning the expression and biological mechanisms of lncRNA-DANCR in tumour development. The related studies were obtained through a systematic search of PubMed, Embase and Cochrane Library. Long non-coding RNAs-DANCR is a valuable cancer-related lncRNA that its dysregulated expression was found in a variety of malignancies, including hepatocellular carcinoma, breast cancer, glioma, colorectal cancer, gastric cancer, and lung cancer. The aberrant expressions of DANCR have been shown to contribute to proliferation, migration and invasion of cancer cells. Long non-coding RNAs-DANCR likely serves as a useful disease biomarker or therapeutic cancer target. Copyright © 2018 Elsevier GmbH. All rights reserved.

Prehospital Blood Product Administration Opportunities in Ground Transport ALS EMS - A Descriptive Study.

PubMed

Mix, Felicia M; Zielinski, Martin D; Myers, Lucas A; Berns, Kathy S; Luke, Anurahda; Stubbs, James R; Zietlow, Scott P; Jenkins, Donald H; Sztajnkrycer, Matthew D

2018-06-01

IntroductionHemorrhage remains the major cause of preventable death after trauma. Recent data suggest that earlier blood product administration may improve outcomes. The purpose of this study was to determine whether opportunities exist for blood product transfusion by ground Emergency Medical Services (EMS). This was a single EMS agency retrospective study of ground and helicopter responses from January 1, 2011 through December 31, 2015 for adult trauma patients transported from the scene of injury who met predetermined hemodynamic (HD) parameters for potential transfusion (heart rate [HR]≥120 and/or systolic blood pressure [SBP]≤90). A total of 7,900 scene trauma ground transports occurred during the study period. Of 420 patients meeting HD criteria for transfusion, 53 (12.6%) had a significant mechanism of injury (MOI). Outcome data were available for 51 patients; 17 received blood products during their emergency department (ED) resuscitation. The percentage of patients receiving blood products based upon HD criteria ranged from 1.0% (HR) to 5.9% (SBP) to 38.1% (HR+SBP). In all, 74 Helicopter EMS (HEMS) transports met HD criteria for blood transfusion, of which, 28 patients received prehospital blood transfusion. Statistically significant total patient care time differences were noted for both the HR and the SBP cohorts, with HEMS having longer time intervals; no statistically significant difference in mean total patient care time was noted in the HR+SBP cohort. In this study population, HD parameters alone did not predict need for ED blood product administration. Despite longer transport times, only one-third of HEMS patients meeting HD criteria for blood administration received prehospital transfusion. While one-third of ground Advanced Life Support (ALS) transport patients manifesting HD compromise received blood products in the ED, this represented 0.2% of total trauma transports over the study period. Given complex logistical issues involved in

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term

PubMed Central

Romero, Roberto; Tarca, Adi; Chaemsaithong, Piya; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Jia, Hui; Hassan, Sonia S.; Kalita, Cynthia A.; Cai, Juan; Yeo, Lami; Lipovich, Leonard

2014-01-01

Objective The mechanisms responsible for normal and abnormal parturition are poorly understood. Myometrial activation leading to regular uterine contractions is a key component of labor. Dysfunctional labor (arrest of dilatation and/or descent) is a leading indication for cesarean delivery. Compelling evidence suggests that most of these disorders are functional in nature, and not the result of cephalopelvic disproportion. The methodology and the datasets afforded by the post-genomic era provide novel opportunities to understand and target gene functions in these disorders. In 2012, the ENCODE Consortium elucidated the extraordinary abundance and functional complexity of long non-coding RNA genes in the human genome. The purpose of the study was to identify differentially expressed long non-coding RNA genes in human myometrium in women in spontaneous labor at term. Materials and Methods Myometrium was obtained from women undergoing cesarean deliveries who were not in labor (n=19) and women in spontaneous labor at term (n=20). RNA was extracted and profiled using an Illumina® microarray platform. The analysis of the protein coding genes from this study has been previously reported. Here, we have used computational approaches to bound the extent of long non-coding RNA representation on this platform, and to identify co-differentially expressed and correlated pairs of long non-coding RNA genes and protein-coding genes sharing the same genomic loci. Results Upon considering more than 18,498 distinct lncRNA genes compiled nonredundantly from public experimental data sources, and interrogating 2,634 that matched Illumina microarray probes, we identified co-differential expression and correlation at two genomic loci that contain coding-lncRNA gene pairs: SOCS2-AK054607 and LMCD1-NR_024065 in women in spontaneous labor at term. This co-differential expression and correlation was validated by qRT-PCR, an independent experimental method. Intriguingly, one of the two lnc

Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline.

PubMed

Toffano-Nioche, Claire; Luo, Yufei; Kuchly, Claire; Wallon, Claire; Steinbach, Delphine; Zytnicki, Matthias; Jacq, Annick; Gautheret, Daniel

2013-09-01

RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Variation in conserved non-coding sequences on chromosome 5q andsusceptibility to asthma and atopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donfack, Joseph; Schneider, Daniel H.; Tan, Zheng

2005-09-10

Background: Evolutionarily conserved sequences likely havebiological function. Methods: To determine whether variation in conservedsequences in non-coding DNA contributes to risk for human disease, westudied six conserved non-coding elements in the Th2 cytokine cluster onhuman chromosome 5q31 in a large Hutterite pedigree and in samples ofoutbred European American and African American asthma cases and controls.Results: Among six conserved non-coding elements (>100 bp,>70percent identity; human-mouse comparison), we identified one singlenucleotide polymorphism (SNP) in each of two conserved elements and sixSNPs in the flanking regions of three conserved elements. We genotypedour samples for four of these SNPs and an additional three SNPs eachmore » inthe IL13 and IL4 genes. While there was only modest evidence forassociation with single SNPs in the Hutterite and European Americansamples (P<0.05), there were highly significant associations inEuropean Americans between asthma and haplotypes comprised of SNPs in theIL4 gene (P<0.001), including a SNP in a conserved non-codingelement. Furthermore, variation in the IL13 gene was strongly associatedwith total IgE (P = 0.00022) and allergic sensitization to mold allergens(P = 0.00076) in the Hutterites, and more modestly associated withsensitization to molds in the European Americans and African Americans (P<0.01). Conclusion: These results indicate that there is overalllittle variation in the conserved non-coding elements on 5q31, butvariation in IL4 and IL13, including possibly one SNP in a conservedelement, influence asthma and atopic phenotypes in diversepopulations.« less

Blood temperature and perfusion to exercising and non-exercising human limbs.

PubMed

González-Alonso, José; Calbet, José A L; Boushel, Robert; Helge, Jørn W; Søndergaard, Hans; Munch-Andersen, Thor; van Hall, Gerrit; Mortensen, Stefan P; Secher, Niels H

2015-10-01

What is the central question of this study? Temperature-sensitive mechanisms are thought to contribute to blood-flow regulation, but the relationship between exercising and non-exercising limb perfusion and blood temperature is not established. What is the main finding and its importance? The close coupling among perfusion, blood temperature and aerobic metabolism in exercising and non-exercising extremities across different exercise modalities and activity levels and the tight association between limb vasodilatation and increases in plasma ATP suggest that both temperature- and metabolism-sensitive mechanisms are important for the control of human limb perfusion, possibly by activating ATP release from the erythrocytes. Temperature-sensitive mechanisms may contribute to blood-flow regulation, but the influence of temperature on perfusion to exercising and non-exercising human limbs is not established. Blood temperature (TB ), blood flow and oxygen uptake (V̇O2) in the legs and arms were measured in 16 healthy humans during 90 min of leg and arm exercise and during exhaustive incremental leg or arm exercise. During prolonged exercise, leg blood flow (LBF) was fourfold higher than arm blood flow (ABF) in association with higher TB and limb V̇O2. Leg and arm vascular conductance during exercise compared with rest was related closely to TB (r(2) = 0.91; P < 0.05), plasma ATP (r(2) = 0.94; P < 0.05) and limb V̇O2 (r(2) = 0.99; P < 0.05). During incremental leg exercise, LBF increased in association with elevations in TB and limb V̇O2, whereas ABF, arm TB and V̇O2 remained largely unchanged. During incremental arm exercise, both ABF and LBF increased in relationship to similar increases in V̇O2. In 12 trained males, increases in femoral TB and LBF during incremental leg exercise were mirrored by similar pulmonary artery TB and cardiac output dynamics, suggesting that processes in active limbs dominate central temperature and perfusion responses. The present data

Impact of sickle cell trait on the thrombotic risk associated with non-O blood groups in northern Nigeria.

PubMed

Ahmed, Sagir G; Kagu, Modu B; Ibrahim, Umma A; Bukar, Audu A

2015-10-01

The non-O blood group is an established risk factor for deep vein thrombosis (DVT), while controversy surrounds the role of sickle cell trait (SCT) as a risk factor for DVT. We hypothesised that if SCT is a risk factor for DVT, individuals with non-O blood groups and SCT (Hb AS) would have a higher risk of DVT than their counterparts with non-O blood groups and normal haemoglobin phenotype (Hb AA). We retrospectively analysed the prevalence of SCT and non-O blood groups among 148 DVT patients with control subjects in order to determine the role of SCT as a risk factor for DVT and its impact on the risk of DVT among patients with non-O blood groups. In comparison with control subjects, DVT patients had significantly higher prevalences of SCT (35.1% vs 27.7%, p=0.04) and non-O blood groups (68.9% vs 45.9%, p=0.02). The odds ratios for DVT due to SCT, non-O blood groups with normal Hb phenotype (Hb AA) and non-O blood groups with SCT (Hb AS) were 1.3, 2.4 and 3.5, respectively. These results suggest that SCT by itself is a weak risk factor for DVT but it has the potential of escalating the DVT risk among patients with non-O blood groups. The combined effects of elevated clotting factors (non-O group effect) and increased clotting factor activation (SCT effect) were responsible for the escalated DVT risk among patients with co-inheritance of non-O blood groups and SCT. Co-inheritance of SCT and non-O blood group is, therefore, an important mixed risk factor for DVT. This should be taken into account when assessing DVT risk profiles of patients in Africa and other parts of the world where the SCT is prevalent.

The long non-coding RNA LSINCT5 promotes malignancy in non-small cell lung cancer by stabilizing HMGA2.

PubMed

Tian, Yuheng; Zhang, Lina; Chen, Shuwen; Ma, Yuan; Liu, Yanyan

2018-06-08

Long non-coding RNAs (lncRNAs) can actively participate in tumorigenesis in various cancers. However, the involvement of lncRNA long stress induced non-coding transcripts 5 (LSINCT5) in non-small cell lung cancer (NSCLC) remains largely unknown. Here we showed a novel lncRNA signature in NSCLC through lncRNA profiling. Increased LSINCT5 expression positively correlates with malignant clinicopathological features and poor survival. LSINCT5 can promote migration and viability of various NSCLC cells in vitro and also enhance lung cancer progression in vivo. RNA immunoprecipitation followed by mass spectrometry has identified that LSINCT5 interacts with HMGA2. This physical interaction can increase the stability of HMGA2 by inhibiting proteasome-mediated degradation. Therefore, LSINCT5 may possibly contribute to NSCLC tumorigenesis by stabilizing the oncogenic factor of HMGA2. This novel LSINCT5/HMGA2 axis can modulate lung cancer progression and might be a promising target for pharmacological intervention.

Infusion of a non-HLA-matched ex-vivo expanded cord blood progenitor cell product after intensive acute myeloid leukaemia chemotherapy: a phase 1 trial.

PubMed

Delaney, Colleen; Milano, Filippo; Cicconi, Laura; Othus, Megan; Becker, Pamela S; Sandhu, Vicky; Nicoud, Ian; Dahlberg, Ann; Bernstein, Irwin D; Appelbaum, Frederick R; Estey, Elihu H

2016-07-01

The intensive chemotherapy regimens used to treat acute myeloid leukaemia routinely result in serious infections, largely due to prolonged neutropenia. We investigated the use of non-HLA-matched ex-vivo expanded cord blood progenitor cells to accelerate haemopoietic recovery and reduce infections after chemotherapy. We enrolled patients with a diagnosis of acute myeloid leukaemia by WHO criteria and aged 18-70 years inclusive at our institution (Fred Hutchinson Cancer Research Center) into this phase 1 trial. The primary endpoint of the study was safety of infusion of non-HLA-matched expanded cord blood progenitor cells after administration of clofarabine, cytarabine, and granulocyte-colony stimulating factor priming. The protocol is closed to accrual and analysis was performed per protocol. The trial is registered with ClinicalTrials.gov, NCT01031368. Between June 29, 2010, and June 26, 2012, 29 patients with acute myeloid leukaemia (19 newly diagnosed, ten relapsed or refractory) were enrolled. The most common adverse events were fever (27 [93%] of 29 patients) and infections (25 [86%] of 29 patients). We observed one case of acute infusional toxicity (attributed to an allergic reaction to dimethyl sulfoxide) in the 29 patients enrolled, who received 42 infusions of expanded progenitor cells. The following additional serious but expected adverse events were observed (each in one patient): grade 4 atrial fibrillation, grade 4 febrile neutropenia, lung infection with grade 4 absolute neutrophil count, colon infection with grade 4 absolute neutrophil count, grade 4 changed mental status, and one death from liver failure. No unexpected toxicity or graft-versus-host disease was observed. There was no evidence of in-vivo persistence of the expanded progenitor cell product in any patient beyond 14 days or induced alloimmunisation. Infusion of the expanded progenitor cell product seemed safe and might provide a promising treatment method for patients with acute myeloid

Simulation-optimization model for production planning in the blood supply chain.

PubMed

Osorio, Andres F; Brailsford, Sally C; Smith, Honora K; Forero-Matiz, Sonia P; Camacho-Rodríguez, Bernardo A

2017-12-01

Production planning in the blood supply chain is a challenging task. Many complex factors such as uncertain supply and demand, blood group proportions, shelf life constraints and different collection and production methods have to be taken into account, and thus advanced methodologies are required for decision making. This paper presents an integrated simulation-optimization model to support both strategic and operational decisions in production planning. Discrete-event simulation is used to represent the flows through the supply chain, incorporating collection, production, storing and distribution. On the other hand, an integer linear optimization model running over a rolling planning horizon is used to support daily decisions, such as the required number of donors, collection methods and production planning. This approach is evaluated using real data from a blood center in Colombia. The results show that, using the proposed model, key indicators such as shortages, outdated units, donors required and cost are improved.

21 CFR 607.7 - Establishment registration and product listing of blood banks and other firms manufacturing human...

Code of Federal Regulations, 2013 CFR

2013-04-01

... blood banks and other firms manufacturing human blood and blood products. 607.7 Section 607.7 Food and... ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS General Provisions § 607.7 Establishment registration and product listing of blood banks and other firms...

21 CFR 607.7 - Establishment registration and product listing of blood banks and other firms manufacturing human...

Code of Federal Regulations, 2012 CFR

2012-04-01

... blood banks and other firms manufacturing human blood and blood products. 607.7 Section 607.7 Food and... ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS General Provisions § 607.7 Establishment registration and product listing of blood banks and other firms...

21 CFR 607.7 - Establishment registration and product listing of blood banks and other firms manufacturing human...

Code of Federal Regulations, 2014 CFR

2014-04-01

... blood banks and other firms manufacturing human blood and blood products. 607.7 Section 607.7 Food and... ESTABLISHMENT REGISTRATION AND PRODUCT LISTING FOR MANUFACTURERS OF HUMAN BLOOD AND BLOOD PRODUCTS General Provisions § 607.7 Establishment registration and product listing of blood banks and other firms...

[Logistic and production process in a regional blood center: modeling and analysis].

PubMed

Baesler, Felipe; Martínez, Cristina; Yaksic, Eduardo; Herrera, Claudia

2011-09-01

The blood supply chain is a complex system that considers different interconnected elements that have to be synchronized correctly to satisfy in quality and quantity the final patient requirements. To determine the blood center maximum production capacity, as well as the determination of the necessary changes for a future production capacity expansion. This work was developed in the Blood Center of Concepción, Chile, operations management tools were applied to model it and to propose improvement alternatives for the production process. The use of simulation is highlighted, which permitted the replication of the center behavior and the evaluation of expansion alternatives. It is possible to absorb a 100% increment in blood demand, without making major changes or investments in the production process. Also it was possible to determine the subsequent steps in terms of investments in equipment and human resources for a future expansion of the center coverage. The techniques used to model the production process of the blood center of Concepción, Chile, allowed us to analyze how it operates, to detect "bottle necks", and to support the decision making process for a future expansion of its capacity.

Extension of Murray's law using a non-Newtonian model of blood flow.

PubMed

Revellin, Rémi; Rousset, François; Baud, David; Bonjour, Jocelyn

2009-05-15

So far, none of the existing methods on Murray's law deal with the non-Newtonian behavior of blood flow although the non-Newtonian approach for blood flow modelling looks more accurate. MODELING: In the present paper, Murray's law which is applicable to an arterial bifurcation, is generalized to a non-Newtonian blood flow model (power-law model). When the vessel size reaches the capillary limitation, blood can be modeled using a non-Newtonian constitutive equation. It is assumed two different constraints in addition to the pumping power: the volume constraint or the surface constraint (related to the internal surface of the vessel). For a seek of generality, the relationships are given for an arbitrary number of daughter vessels. It is shown that for a cost function including the volume constraint, classical Murray's law remains valid (i.e. SigmaR(c) = cste with c = 3 is verified and is independent of n, the dimensionless index in the viscosity equation; R being the radius of the vessel). On the contrary, for a cost function including the surface constraint, different values of c may be calculated depending on the value of n. We find that c varies for blood from 2.42 to 3 depending on the constraint and the fluid properties. For the Newtonian model, the surface constraint leads to c = 2.5. The cost function (based on the surface constraint) can be related to entropy generation, by dividing it by the temperature. It is demonstrated that the entropy generated in all the daughter vessels is greater than the entropy generated in the parent vessel. Furthermore, it is shown that the difference of entropy generation between the parent and daughter vessels is smaller for a non-Newtonian fluid than for a Newtonian fluid.

Distribution of di(2-ethylhexyl) phthalate and products in blood and blood components.

PubMed Central

Rock, G; Labow, R S; Tocchi, M

1986-01-01

In order to impart flexibility, plastic medical devices incorporate liquid plasticizers into their structure. Data from several laboratories, including ours, have shown that these compounds leach from blood bags and tubing during collection of blood, storage of various blood components and during kidney dialysis and cell and plasma apheresis procedures. After the plasticizer di(2-ethylhexyl) phthalate leaches from poly(vinyl chloride) blood packs, it is converted by a plasma enzyme to a more toxic metabolite, mono(2-ethylhexyl) phthalate. Blood fractionation products from outdated plasma contain mono(2-ethylhexyl) phthalate, the highest level being found in normal serum albumin. Recently, we have reported that di(2-ethylhexyl) phthalate actually binds to the red blood cell membrane and reduces its osmotic fragility. Current methods of red cells storage, which permit utilization up to 35 days after collection, are not possible without this membrane stabilization. Platelets are now stored for 5 days in the Fenwal PL 732 polyolefin bag. Although stated to be essentially free of liquid plasticizers, a significant level of leaching from this bag into the extracts of stored platelet concentrates was observed. PMID:3709456

Automatic detection of blood versus non-blood regions on intravascular ultrasound (IVUS) images using wavelet packet signatures

NASA Astrophysics Data System (ADS)

Katouzian, Amin; Baseri, Babak; Konofagou, Elisa E.; Laine, Andrew F.

2008-03-01

Intravascular ultrasound (IVUS) has been proven a reliable imaging modality that is widely employed in cardiac interventional procedures. It can provide morphologic as well as pathologic information on the occluded plaques in the coronary arteries. In this paper, we present a new technique using wavelet packet analysis that differentiates between blood and non-blood regions on the IVUS images. We utilized the multi-channel texture segmentation algorithm based on the discrete wavelet packet frames (DWPF). A k-mean clustering algorithm was deployed to partition the extracted textural features into blood and non-blood in an unsupervised fashion. Finally, the geometric and statistical information of the segmented regions was used to estimate the closest set of pixels to the lumen border and a spline curve was fitted to the set. The presented algorithm may be helpful in delineating the lumen border automatically and more reliably prior to the process of plaque characterization, especially with 40 MHz transducers, where appearance of the red blood cells renders the border detection more challenging, even manually. Experimental results are shown and they are quantitatively compared with manually traced borders by an expert. It is concluded that our two dimensional (2-D) algorithm, which is independent of the cardiac and catheter motions performs well in both in-vivo and in-vitro cases.

Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis.

PubMed

Herdewyn, Sarah; Zhao, Hui; Moisse, Matthieu; Race, Valérie; Matthijs, Gert; Reumers, Joke; Kusters, Benno; Schelhaas, Helenius J; van den Berg, Leonard H; Goris, An; Robberecht, Wim; Lambrechts, Diether; Van Damme, Philip

2012-06-01

Motor neuron degeneration in amyotrophic lateral sclerosis (ALS) has a familial cause in 10% of patients. Despite significant advances in the genetics of the disease, many families remain unexplained. We performed whole-genome sequencing in five family members from a pedigree with autosomal-dominant classical ALS. A family-based elimination approach was used to identify novel coding variants segregating with the disease. This list of variants was effectively shortened by genotyping these variants in 2 additional unaffected family members and 1500 unrelated population-specific controls. A novel rare coding variant in SPAG8 on chromosome 9p13.3 segregated with the disease and was not observed in controls. Mutations in SPAG8 were not encountered in 34 other unexplained ALS pedigrees, including 1 with linkage to chromosome 9p13.2-23.3. The shared haplotype containing the SPAG8 variant in this small pedigree was 22.7 Mb and overlapped with the core 9p21 linkage locus for ALS and frontotemporal dementia. Based on differences in coverage depth of known variable tandem repeat regions between affected and non-affected family members, the shared haplotype was found to contain an expanded hexanucleotide (GGGGCC)(n) repeat in C9orf72 in the affected members. Our results demonstrate that rare coding variants identified by whole-genome sequencing can tag a shared haplotype containing a non-coding pathogenic mutation and that changes in coverage depth can be used to reveal tandem repeat expansions. It also confirms (GGGGCC)n repeat expansions in C9orf72 as a cause of familial ALS.

Long Non-coding RNAs and Their Biological Roles in Plants

PubMed Central

Liu, Xue; Hao, Lili; Li, Dayong; Zhu, Lihuang; Hu, Songnian

2015-01-01

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants. PMID:25936895

Concentrations of pentosidine, an advanced glycation end-product, in umbilical cord blood.

PubMed

Tsukahara, Hirokazu; Ohta, Naoko; Sato, Shuko; Hiraoka, Masahiro; Shukunami, Ken-Ichi; Uchiyama, Mayumi; Kawakami, Hisako; Sekine, Kyouichi; Mayumi, Mitsufumi

2004-07-01

Advanced glycation end-products (AGEs) are formed over several weeks to months by non-enzymatic glycation and oxidation ("glycoxidation") reactions between carbohydrate-derived carbonyl groups and protein amino groups, known as the Maillard reaction. Pentosidine is one of the best-characterized AGEs and is accepted as a satisfactory marker for glycoxidation in vivo. The present study was intended to measure pentosidine concentrations in umbilical cord blood from newborns with various gestational ages using our recently established high-performance liquid chromatography method [Tsukahara, H. et al. (2003) Pediatr. Res. 54, 419-424]. Our study demonstrates, for the first time, that pentosidine is detected in most of the umbilical blood samples. This study also shows that the umbilical blood concentrations of pentosidine are considerably lower than normal adult values, but that they increase with gestation progression and fetal growth. Umbilical pentosidine concentrations were significantly elevated in newborns of mothers with preeclampsia compared to those of mothers without preeclampsia. We conclude that accumulation of AGEs and oxidative stress occurs in fetal tissues and organs in utero at the early stage of human life and that their accumulation is augmented in the maternal preeclampsic condition.

21 CFR 20.115 - Product codes for manufacturing or sales dates.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Product codes for manufacturing or sales dates. 20.115 Section 20.115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... the label or in labeling or otherwise used in connection with a product subject to the jurisdiction of...

Hydroxyurea for reducing blood transfusion in non-transfusion dependent beta thalassaemias.

PubMed

Foong, Wai Cheng; Ho, Jacqueline J; Loh, C Khai; Viprakasit, Vip

2016-10-18

Non-transfusion dependent beta thalassaemia is a subset of inherited haemoglobin disorders characterised by reduced production of the beta globin chain of the haemoglobin molecule leading to anaemia of varying severity. Although blood transfusion is not a necessity for survival, it is required when episodes of chronic anaemia occur. This chronic anaemia can impair growth and affect quality of life. People with non-transfusion dependent beta thalassaemia suffer from iron overload due to their body's increased capability of absorbing iron from food sources. Iron overload becomes more pronounced in those requiring blood transfusion. People with a higher foetal haemoglobin level have been found to require fewer blood transfusions. Hydroxyurea has been used to increase foetal haemoglobin level; however, its efficacy in reducing transfusion, chronic anaemia complications and its safety need to be established. To assess the effectiveness, safety and appropriate dose regimen of hydroxyurea in people with non-transfusion dependent beta thalassaemia (haemoglobin E combined with beta thalassaemia and beta thalassaemia intermedia). We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Haemoglobinopathies Trials Register, compiled from electronic database searches and handsearching of relevant journals. We also searched ongoing trials registries and the reference lists of relevant articles and reviews.Date of last search: 30 April 2016. Randomised or quasi-randomised controlled trials of hydroxyurea in people with non-transfusion dependent beta thalassaemia comparing hydroxyurea with placebo or standard treatment or comparing different doses of hydroxyurea. Two authors independently applied the inclusion criteria in order to select trials for inclusion. Both authors assessed the risk of bias of trials and extracted the data. A third author verified these assessments. No trials comparing hydroxyurea with placebo or standard care were found. However, we included

Comparison study of upper arm and forearm non-invasive blood pressures in adult Emergency Department patients.

PubMed

Schimanski, Karen; Jull, Andrew; Mitchell, Nancy; McLay, Jessica

2014-12-01

Forearm blood pressures have been suggested as an alternative site to measure blood pressures when the upper arm is unavailable. However there is little evidence utilising clinical populations to support this substitution. To determine agreement between blood pressures measured in the left upper arm and forearm using a singular oscillometric non-invasive device in adult Emergency Department patients. The secondary objective was to explore the relationship of blood pressure differences with age, sex, ethnicity, smoking history and obesity. Single centre comparison study. Adult Emergency Department, Tertiary Trauma Centre. Forty-four participants who met inclusion/exclusion criteria selected sequentially from the Emergency Department arrival board. A random assignment of order of measurement for left upper arm and forearm blood pressures was utilised. Participants were eligible if they were aged 18 years or older, had been assigned an Australasian Triage Scale code of 2, 3, 4, or 5, were able to consent, and able to have blood pressures measured on their left arm whilst lying at a 45° angle. The Bland-Altman method of statistical analysis was used, with the level of agreement for clinical acceptability for the systolic, diastolic and mean arterial pressure defined as ±10 mmHg. The forearm measure overestimated systolic (mean difference 2.2 mmHg, 95% limits of agreement ±19 mmHg), diastolic (mean difference 3.4 mmHg, 95% limits of agreement ±14.4 mmHg), and mean arterial pressures (mean difference 4.1 mmHg, 95% limits of agreement ±13.7 mmHg). The systolic measure was not significantly different from zero. Evidence of better agreement was found with upper arm/forearm systolic measures below 140 mmHg compared to systolic measures above 140 mmHg using the Levene's test (p=0.002, F-statistic=11.09). Blood pressure disparity was not associated with participant characteristics. Forearm measures cannot routinely replace upper arm measures for blood pressure measurement

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

PubMed

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

9 CFR 310.20 - Saving of blood from livestock as an edible product.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Saving of blood from livestock as an... AND VOLUNTARY INSPECTION AND CERTIFICATION POST-MORTEM INSPECTION § 310.20 Saving of blood from livestock as an edible product. Blood may be saved for edible purposes at official establishments provided...

9 CFR 310.20 - Saving of blood from livestock as an edible product.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Saving of blood from livestock as an... AND VOLUNTARY INSPECTION AND CERTIFICATION POST-MORTEM INSPECTION § 310.20 Saving of blood from livestock as an edible product. Blood may be saved for edible purposes at official establishments provided...

9 CFR 310.20 - Saving of blood from livestock as an edible product.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Saving of blood from livestock as an... AND VOLUNTARY INSPECTION AND CERTIFICATION POST-MORTEM INSPECTION § 310.20 Saving of blood from livestock as an edible product. Blood may be saved for edible purposes at official establishments provided...

9 CFR 310.20 - Saving of blood from livestock as an edible product.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Saving of blood from livestock as an... AND VOLUNTARY INSPECTION AND CERTIFICATION POST-MORTEM INSPECTION § 310.20 Saving of blood from livestock as an edible product. Blood may be saved for edible purposes at official establishments provided...

9 CFR 310.20 - Saving of blood from livestock as an edible product.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Saving of blood from livestock as an... AND VOLUNTARY INSPECTION AND CERTIFICATION POST-MORTEM INSPECTION § 310.20 Saving of blood from livestock as an edible product. Blood may be saved for edible purposes at official establishments provided...

Solving Mendelian Mysteries: The Non-coding Genome May Hold the Key.

PubMed

Valente, Enza Maria; Bhatia, Kailash P

2018-02-22

Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism. Copyright © 2018 Elsevier Inc. All rights reserved.

Non-Newtonian effects of blood flow on hemodynamics in distal vascular graft anastomoses.

PubMed

Chen, Jie; Lu, Xi-Yun; Wang, Wen

2006-01-01

Non-Newtonian fluid flow in a stenosed coronary bypass is investigated numerically using the Carreau-Yasuda model for the shear thinning behavior of the blood. End-to-side coronary bypass anastomosis is considered in a simplified model geometry where the host coronary artery has a 75% severity stenosis. Different locations of the bypass graft to the stenosis and different flow rates in the graft and in the host artery are studied. Particular attention is given to the non-Newtonian effect of the blood on the primary and secondary flow patterns in the host coronary artery and the wall shear stress (WSS) distribution there. Interaction between the jet flow from the stenosed artery and the flow from the graft is simulated by solving the three-dimensional Navier-Stokes equation coupled with the non-Newtonian constitutive model. Results for the non-Newtonian flow, the Newtonian flow and the rescaled Newtonian flow are presented. Significant differences in axial velocity profiles, secondary flow streamlines and WSS between the non-Newtonian and Newtonian fluid flows are revealed. However, reasonable agreement between the non-Newtonian and the rescaled Newtonian flows is found. Results from this study support the view that the residual flow in a partially occluded coronary artery interacts with flow in the bypass graft and may have significant hemodynamic effects in the host vessel downstream of the graft. Non-Newtonian property of the blood alters the flow pattern and WSS distribution and is an important factor to be considered in simulating hemodynamic effects of blood flow in arterial bypass grafts.

Long Non-Coding RNA CASC2 Improves Diabetic Nephropathy by Inhibiting JNK Pathway.

PubMed

Yang, Huihui; Kan, Quan E; Su, Yong; Man, Hua

2018-06-11

It's known that long non-coding RNA CASC2 overexpression inhibit the JNK pathway in some disease models, while JNK pathway activation exacerbates diabetic nephropathy. Therefore we speculate that long non-coding RNA CASC2 can improve diabetic nephropathy by inhibiting JNK pathway. Thus, our study was carried out to investigate the involvement of CASC2 in diabetic nephropathy. We found that serum level of CASC2 was significantly lower in diabetic nephropathy patients than in normal people, and serum level of CASC2 showed no significant correlations with age, gender, alcohol consumption and smoking habits, but was correlated with course of disease. ROC curve analysis showed that serum level of CASC2 could be used to accurately predict diabetic nephropathy. Diabetes mellitus has many complications. This study also included a series of complications of diabetes, such as diabetic retinopathy, diabetic ketoacidosis, diabetic foot infections and diabetic cardiopathy, while serum level of CASC2 was specifically reduced in diabetic nephropathy. CASC2 expression level decreased, while JNK1 phosphorylation level increased in mouse podocyte cells treated with high glucose. CASC2 overexpression inhibited apoptosis of podocyte cells and reduced phosphorylation level of JNK1. We conclude that long non-coding RNA CASC2 may improve diabetic nephropathy by inhibiting JNK pathway. © Georg Thieme Verlag KG Stuttgart · New York.

Non-terminal blood sampling techniques in guinea pigs.

PubMed

Birck, Malene M; Tveden-Nyborg, Pernille; Lindblad, Maiken M; Lykkesfeldt, Jens

2014-10-11

Guinea pigs possess several biological similarities to humans and are validated experimental animal models(1-3). However, the use of guinea pigs currently represents a relatively narrow area of research and descriptive data on specific methodology is correspondingly scarce. The anatomical features of guinea pigs are slightly different from other rodent models, hence modulation of sampling techniques to accommodate for species-specific differences, e.g., compared to mice and rats, are necessary to obtain sufficient and high quality samples. As both long and short term in vivo studies often require repeated blood sampling the choice of technique should be well considered in order to reduce stress and discomfort in the animals but also to ensure survival as well as compliance with requirements of sample size and accessibility. Venous blood samples can be obtained at a number of sites in guinea pigs e.g., the saphenous and jugular veins, each technique containing both advantages and disadvantages(4,5). Here, we present four different blood sampling techniques for either conscious or anaesthetized guinea pigs. The procedures are all non-terminal procedures provided that sample volumes and number of samples do not exceed guidelines for blood collection in laboratory animals(6). All the described methods have been thoroughly tested and applied for repeated in vivo blood sampling in studies within our research facility.

Study of microvascular non-Newtonian blood flow modulated by electroosmosis.

PubMed

Tripathi, Dharmendra; Yadav, Ashu; Anwar Bég, O; Kumar, Rakesh

2018-05-01

An analytical study of microvascular non-Newtonian blood flow is conducted incorporating the electro-osmosis phenomenon. Blood is considered as a Bingham rheological aqueous ionic solution. An externally applied static axial electrical field is imposed on the system. The Poisson-Boltzmann equation for electrical potential distribution is implemented to accommodate the electrical double layer in the microvascular regime. With long wavelength, lubrication and Debye-Hückel approximations, the boundary value problem is rendered non-dimensional. Analytical solutions are derived for the axial velocity, volumetric flow rate, pressure gradient, volumetric flow rate, averaged volumetric flow rate along one time period, pressure rise along one wavelength and stream function. A plug swidth is featured in the solutions. Via symbolic software (Mathematica), graphical plots are generated for the influence of Bingham plug flow width parameter, electrical Debye length and Helmholtz-Smoluchowski velocity (maximum electro-osmotic velocity) on the key hydrodynamic variables. This study reveals that blood flow rate accelerates with decreasing the plug width (i.e. viscoplastic nature of fluids) and also with increasing the Debye length parameter. Copyright © 2018 Elsevier Inc. All rights reserved.

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

50 CFR Table 3c to Part 680 - Crab Product Codes for Economic Data Reports

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Crab Product Codes for Economic Data Reports 3c Table 3c to Part 680 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL... EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 680, Table 3c Table 3c to Part 680—Crab Product Codes for Economic...

Non-invasive blood glucose monitor based on spectroscopy using a smartphone.

PubMed

Dantu, Vishnu; Vempati, Jagannadh; Srivilliputhur, Srinivasan

2014-01-01

Development of a novel method for non-invasive measurement of blood glucose concentration using smartphone is discussed. Our research work has three major contributions to society and science. First, we modified and extended the Beer-Lambert's law in physics to accommodate for multiple wavelengths. This extension can aid researchers who wish to perform optical spectroscopy. Second, we successfully developed a creative and non-invasive way for diabetic patients to measure glucose levels via a smartphone. Researchers and chemists can now use their smartphones to determine the absorbance and, therefore, concentration of a chemical. Third, we created an inexpensive way to perform optical spectroscopy by using a smartphone. Monitoring blood glucose using a smartphone application that simply uses equipment already available on smartphones will improve the lives of diabetic patients who can continuously check their blood glucose levels while avoiding the current inconvenient, unhygienic, and costly invasive glucose meters.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

PubMed

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2017-12-20

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

PubMed Central

Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

2017-01-01

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

Internal quality control of blood products: An experience from a tertiary care hospital blood bank from Southern Pakistan.

PubMed

Sultan, Sadia; Zaheer, Hasan Abbas; Waheed, Usman; Baig, Mohammad Amjad; Rehan, Asma; Irfan, Syed Mohammed

2018-01-01

Internal quality control (IQC) is the backbone of quality assurance program. In blood banking, the quality control of blood products ensures the timely availability of a blood component of high quality with maximum efficacy and minimal risk to potential recipients. The main objective of this study is to analyze the IQC of blood products as an indicator of our blood bank performance. An observational cross-sectional study was conducted at the blood bank of Liaquat National Hospital and Medical College, from January 2014 to December 2015. A total of 100 units of each blood components were arbitrarily chosen during the study. Packed red cell units were evaluated for hematocrit (HCT); random platelet concentrates were evaluated for pH, yield, and culture; fresh frozen plasma (FFP) and cryoprecipitate (CP) were evaluated for unit volume, factor VIII, and fibrinogen concentrations. A total of 400 units were tested for IQC. The mean HCT of packed red cells was 69.5 ± 7.24, and in 98% units, it met the standard (<80% of HCT). The mean platelet yield was 8.8 ± 3.40 × 10 9 /L and pH was ≥6.2 in 98% bags; cultures were negative in 97% of units tested. Mean factor VIII and fibrinogen levels were found to be 84.24 ± 15.01 and 247.17 ± 49.69 for FFP, respectively. For CP, mean factor VIII and fibrinogen level were found to be 178.75 ± 86.30 and 420.7 ± 75.32, respectively. The IQC of blood products at our blood bank is in overall compliance and met recommended international standards. Implementation of standard operating procedures, accomplishment of standard guidelines, proper documentation with regular audit, and staff competencies can improve the quality performance of the transfusion services.

Gingival blood flow measurement with a non-contact laser flowmeter.

PubMed

Matsuki, M; Xu, Y B; Nagasawa, T

2001-07-01

A non-contact laser flowmeter was used to measure the changing of the gingival blood flow. Five university students with healthy oral condition were selected in this study. The blood flow measurement on the extensor digitorum (above the head of third metacarpal), with the changing of distance and angle between the probe and the tissue was used as a pre-study experiment. Blood flow rate was determined in the labial gingiva (2 mm above the cervical line) of upper central incisor using a stent fixing the probe at a 3-mm distance from the tissue. A basal level of gingival blood flow was taken two times each day for 5 days. The effects of water of different temperatures on the gingival blood flow are discussed. With the changing of distance, the blood flow rate became smaller, but there was no significant effect from the angle. The reproducibility was acceptable through the 5-day measurement. After stimulating with warm and body temperature water, the blood flow first increased significantly and then went back to the basal line (faster with the body temperature water). With cold water, different reactions between the subjects were observed.

Theater Blood Application Was Not Effectively Developed and Implemented

DTIC Science & Technology

2015-07-17

blood product by unit; and • monitor non- Food and Drug Administration Blood Product Testing. The CONOPS document also identified over 400 specific...time of a transfusion. However, this requirement was not identified in the CONOPS document. Further, PEO DHCS officials provided a traceability ...the CONOPS document, requirements management database, and the traceability matrix increased the risk that the Theater Blood Application

LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature.

PubMed

Pian, Cong; Zhang, Guangle; Chen, Zhi; Chen, Yuanyuan; Zhang, Jin; Yang, Tao; Zhang, Liangyun

2016-01-01

As a novel class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been verified to be associated with various diseases. As large scale transcripts are generated every year, it is significant to accurately and quickly identify lncRNAs from thousands of assembled transcripts. To accurately discover new lncRNAs, we develop a classification tool of random forest (RF) named LncRNApred based on a new hybrid feature. This hybrid feature set includes three new proposed features, which are MaxORF, RMaxORF and SNR. LncRNApred is effective for classifying lncRNAs and protein coding transcripts accurately and quickly. Moreover,our RF model only requests the training using data on human coding and non-coding transcripts. Other species can also be predicted by using LncRNApred. The result shows that our method is more effective compared with the Coding Potential Calculate (CPC). The web server of LncRNApred is available for free at http://mm20132014.wicp.net:57203/LncRNApred/home.jsp.

Blood products use in France: a nationwide cross-sectional survey.

PubMed

Fillet, Anne-Marie; Desmarets, Maxime; Assari, Suzanne; Quaranta, Jean-François; François, Anne; Pugin, Aurore; Schuhmacher, Anne; Lassale, Bernard; Monnet, Elisabeth; Cabre, Philippe; Legrand, Dominique; Binda, Delphine; Djoudi, Rachid

2016-12-01

Blood products use has increased in France between 2000 and 2011. To understand the reasons for this increase, data about transfused patients and transfusion practices needed to be updated. A nationwide cross-sectional survey was performed with health care establishments. Diagnoses and indication for the transfusion, pretransfusion laboratory results, and blood products used were collected during a randomly selected 24-hour period in 2011. All patients who received at least one blood product delivered on the survey day were included. A total of 10,794 blood products were requested for 4720 patients: 8688 red blood cell (RBC) units, 842 platelet (PLT) concentrates, and 1264 fresh-frozen plasma (FFP) units. Hematologic and cancer pathologies included 46% of transfused patients, 34% of the patients had transfusions in a surgical context, and 32.4% of transfused patients were receiving medication with an impact on transfusion. Nearly half of RBC transfusions were performed with hemoglobin levels of less than 8 g/dL. PLT transfusions for prophylactic indication were prescribed with PLT counts of less than 20 × 10 9 and 50 × 10 9 /L in 56.9 and 86.6% of patients, respectively. RBCs and PLTs transfusion practices were in agreement with national guidelines. FFP units were involved in 8.0% of all prescriptions. Among these, 57.4% were requested in the context of an acute hemorrhage and 8.4% for plasma exchange. The median of FFP use (n = 2) in a nonsurgical context, excluding plasma exchange, suggests an insufficient dosing of FFP. Except for insufficient FFP dosing per patient and limitations on assessment of indications for prescribing, transfusion practices were in agreement with national guidelines. © 2016 AABB.

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

PubMed Central

Ferlaino, Michael; Rogers, Mark F.; Shihab, Hashem A.; Mort, Matthew; Cooper, David N.; Gaunt, Tom R.; Campbell, Colin

2018-01-01

Background Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. Results We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. Conclusions FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome. PMID:28985712

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

PubMed

Ferlaino, Michael; Rogers, Mark F; Shihab, Hashem A; Mort, Matthew; Cooper, David N; Gaunt, Tom R; Campbell, Colin

2017-10-06

Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.

Follicle vascularity coordinates corpus luteum blood flow and progesterone production.

PubMed

de Tarso, S G S; Gastal, G D A; Bashir, S T; Gastal, M O; Apgar, G A; Gastal, E L

2017-03-01

Colour Doppler ultrasonography was used to compare the ability of preovulatory follicle (POF) blood flow and its dimensions to predict the size, blood flow and progesterone production capability of the subsequent corpus luteum (CL). Cows (n=30) were submitted to a synchronisation protocol. Follicles ≥7mm were measured and follicular wall blood flow evaluated every 12h for approximately 3.5 days until ovulation. After ovulation, cows were scanned daily for 8 days and similar parameters were evaluated for the CL. Blood samples were collected and plasma progesterone concentrations quantified. All parameters were positively correlated. Correlation values ranged from 0.26 to 0.74 on data normalised to ovulation and from 0.31 to 0.74 on data normalised to maximum values. Correlations between calculated ratios of both POF and CL in data normalised to ovulation and to maximum values ranged from moderate (0.57) to strong (0.87). Significant (P<0.0001) linear regression analyses were seen in all comparisons. In conclusion, higher correlations were observed between the dimensions of POF and/or CL and blood flow of both structures, as well as POF and/or CL blood flow with plasma progesterone concentrations of the resultant CL. These findings indicate that follicle vascularity coordinates CL blood flow and progesterone production in synchronised beef cows.

[Factors associated with the satisfaction of prescribers of blood products in Burkina Faso].

PubMed

Sawadogo, S; Kafando, E; Nébié, K; Ouédraogo, A-S; Ouattara, S; Dahourou, H; Fretz, C; Deneys, V

2017-11-01

The National Blood Transfusion Centre, unique operator of blood transfusion in Burkina Faso is engaged into the quality process according to ISO 9001. Therefore, the assessment of customer satisfaction is a main part of its system. Our study conceives "customer satisfaction" as dependant to the perceived service quality based on SERVQUAL model. To identify factors associated with the satisfaction of blood products prescribers in order to help decision-makers for continuous improvement of services. We conducted a cross-sectional survey among prescribers of blood components in Ouagadougou, between February 27 and April 30, 2015. We used an anonymous self-administered questionnaire, including 13 items associated to the 5 dimensions of SERVQUAL model. The different satisfaction gaps were calculated and linear regression was used to determine statistical associations with a significance level of 5%. The return rate was 94.5% about the 256 questionnaires distributed. A total of 30% of respondents were satisfied to very satisfied. The overall global gap of satisfaction was -5.74. The product delivery time, the efficacy and safety of blood products, the medical and clinical support, the pro-activity of the communication, the management of blood products reservation and the satisfaction of needs in blood products were the factors associated with the prescribers' satisfaction. This first study in blood transfusion services in our context was been useful to assess customer satisfaction and identify the main axes on which targeting priority actions in order to effectively use available resources. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.

PubMed

Mu, Chuang; Wang, Ruijia; Li, Tianqi; Li, Yuqiang; Tian, Meilin; Jiao, Wenqian; Huang, Xiaoting; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

2016-08-01

Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.

Hemorheological alterations of red blood cells induced by non-thermal dielectric barrier discharge plasma

NASA Astrophysics Data System (ADS)

Kim, Jeongho; Kim, Jae Hyung; Chang, Boksoon; Choi, Eun Ha; Park, Hun-Kuk

2016-11-01

Atmospheric pressure non-thermal plasma has been introduced in various applications such as wound healing, sterilization of infected tissues, blood coagulation, delicate surgeries, and so on. The non-thermal plasma generates reactive oxygen species (ROS), including ozone. Various groups have reported that the produced ROS influence proliferation and differentiation of cells, as well as apoptosis and growth arrest of tumor cells. In this study, we investigated the effects of non-thermal plasma on rheological characteristics of red blood cells (RBC). We experimentally measured the extent of hemolysis, deformability, and aggregation of red blood cells (RBC) with respect to exposure times of non-thermal plasma. RBC morphology was also examined using field-emission scanning electron microscopy. The absorbance of hemoglobin released from the RBCs increased with increasing exposure time of the non-thermal plasma. Values of the elongation index and aggregation index were shown to decrease significantly with increasing plasma exposure times. Therefore, hemorheological properties of RBCs could be utilized to assess the performance of various non-thermal plasmas.

Understanding the Role of Non-Coding RNAs in Bladder Cancer: From Dark Matter to Valuable Therapeutic Targets

PubMed Central

Pop-Bica, Cecilia; Gulei, Diana; Cojocneanu-Petric, Roxana; Braicu, Cornelia; Petrut, Bogdan; Berindan-Neagoe, Ioana

2017-01-01

The mortality and morbidity that characterize bladder cancer compel this malignancy into the category of hot topics in terms of biomolecular research. Therefore, a better knowledge of the specific molecular mechanisms that underlie the development and progression of bladder cancer is demanded. Tumor heterogeneity among patients with similar diagnosis, as well as intratumor heterogeneity, generates difficulties in terms of targeted therapy. Furthermore, late diagnosis represents an ongoing issue, significantly reducing the response to therapy and, inevitably, the overall survival. The role of non-coding RNAs in bladder cancer emerged in the last decade, revealing that microRNAs (miRNAs) may act as tumor suppressor genes, respectively oncogenes, but also as biomarkers for early diagnosis. Regarding other types of non-coding RNAs, especially long non-coding RNAs (lncRNAs) which are extensively reviewed in this article, their exact roles in tumorigenesis are—for the time being—not as evident as in the case of miRNAs, but, still, clearly suggested. Therefore, this review covers the non-coding RNA expression profile of bladder cancer patients and their validated target genes in bladder cancer cell lines, with repercussions on processes such as proliferation, invasiveness, apoptosis, cell cycle arrest, and other molecular pathways which are specific for the malignant transformation of cells. PMID:28703782

Understanding the Role of Non-Coding RNAs in Bladder Cancer: From Dark Matter to Valuable Therapeutic Targets.

PubMed

Pop-Bica, Cecilia; Gulei, Diana; Cojocneanu-Petric, Roxana; Braicu, Cornelia; Petrut, Bogdan; Berindan-Neagoe, Ioana

2017-07-13

The mortality and morbidity that characterize bladder cancer compel this malignancy into the category of hot topics in terms of biomolecular research. Therefore, a better knowledge of the specific molecular mechanisms that underlie the development and progression of bladder cancer is demanded. Tumor heterogeneity among patients with similar diagnosis, as well as intratumor heterogeneity, generates difficulties in terms of targeted therapy. Furthermore, late diagnosis represents an ongoing issue, significantly reducing the response to therapy and, inevitably, the overall survival. The role of non-coding RNAs in bladder cancer emerged in the last decade, revealing that microRNAs (miRNAs) may act as tumor suppressor genes, respectively oncogenes, but also as biomarkers for early diagnosis. Regarding other types of non-coding RNAs, especially long non-coding RNAs (lncRNAs) which are extensively reviewed in this article, their exact roles in tumorigenesis are-for the time being-not as evident as in the case of miRNAs, but, still, clearly suggested. Therefore, this review covers the non-coding RNA expression profile of bladder cancer patients and their validated target genes in bladder cancer cell lines, with repercussions on processes such as proliferation, invasiveness, apoptosis, cell cycle arrest, and other molecular pathways which are specific for the malignant transformation of cells.

Identification and characterization of long non-coding RNAs in rainbow trout eggs

USDA-ARS?s Scientific Manuscript database

Long non-coding RNAs (lncRNAs) are in general considered as a diverse class of transcripts longer than 200 nucleotides that structurally resemble mRNAs but do not encode proteins. Recent advances in RNA sequencing (RNA-Seq) and bioinformatics methods have provided an opportunity to indentify and ana...

Combined impact of lead, cadmium, polychlorinated biphenyls and non-chemical risk factors on blood pressure in NHANES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, Junenette L., E-mail: petersj@bu.edu; Patricia Fabian, M., E-mail: pfabian@bu.edu; Levy, Jonathan I., E-mail: jonlevy@bu.edu

High blood pressure is associated with exposure to multiple chemical and non-chemical risk factors, but epidemiological analyses to date have not assessed the combined effects of both chemical and non-chemical stressors on human populations in the context of cumulative risk assessment. We developed a novel modeling approach to evaluate the combined impact of lead, cadmium, polychlorinated biphenyls (PCBs), and multiple non-chemical risk factors on four blood pressure measures using data for adults aged ≥20 years from the National Health and Nutrition Examination Survey (1999–2008). We developed predictive models for chemical and other stressors. Structural equation models were applied to accountmore » for complex associations among predictors of stressors as well as blood pressure. Models showed that blood lead, serum PCBs, and established non-chemical stressors were significantly associated with blood pressure. Lead was the chemical stressor most predictive of diastolic blood pressure and mean arterial pressure, while PCBs had a greater influence on systolic blood pressure and pulse pressure, and blood cadmium was not a significant predictor of blood pressure. The simultaneously fit exposure models explained 34%, 43% and 52% of the variance for lead, cadmium and PCBs, respectively. The structural equation models were developed using predictors available from public data streams (e.g., U.S. Census), which would allow the models to be applied to any U.S. population exposed to these multiple stressors in order to identify high risk subpopulations, direct intervention strategies, and inform public policy. - Highlights: • We evaluated joint impact of chemical and non-chemical stressors on blood pressure. • We built predictive models for lead, cadmium and polychlorinated biphenyls (PCBs). • Our approach allows joint evaluation of predictors from population-specific data. • Lead, PCBs and established non-chemical stressors were related to blood pressure. �

Non coding RNAs in vascular disease - from basic science to clinical applications: Scientific update from the Working Group of Myocardial Function of the European Society of Cardiology

PubMed

Fiedler, Jan; Baker, Andrew H; Dimmeler, Stefanie; Heymans, Stephane; Mayr, Manuel; Thum, Thomas

2018-05-23

Non-coding RNAs are increasingly recognized not only as regulators of various biological functions but also as targets for a new generation of RNA therapeutics and biomarkers. We hereby review recent insights relating to non-coding RNAs including microRNAs (e.g. miR-126, miR-146a), long non-coding RNAs (e.g. MIR503HG, GATA6-AS, SMILR) and circular RNAs (e.g. cZNF292) and their role in vascular diseases. This includes identification and therapeutic use of hypoxia-regulated non-coding RNAs and endogenous non-coding RNAs that regulate intrinsic smooth muscle cell signalling, age-related non-coding RNAs and non-coding RNAs involved in the regulation of mitochondrial biology and metabolic control. Finally, we discuss non-coding RNA species with biomarker potential.

Quantification of non-coding RNA target localization diversity and its application in cancers.

PubMed

Cheng, Lixin; Leung, Kwong-Sak

2018-04-01

Subcellular localization is pivotal for RNAs and proteins to implement biological functions. The localization diversity of protein interactions has been studied as a crucial feature of proteins, considering that the protein-protein interactions take place in various subcellular locations. Nevertheless, the localization diversity of non-coding RNA (ncRNA) target proteins has not been systematically studied, especially its characteristics in cancers. In this study, we provide a new algorithm, non-coding RNA target localization coefficient (ncTALENT), to quantify the target localization diversity of ncRNAs based on the ncRNA-protein interaction and protein subcellular localization data. ncTALENT can be used to calculate the target localization coefficient of ncRNAs and measure how diversely their targets are distributed among the subcellular locations in various scenarios. We focus our study on long non-coding RNAs (lncRNAs), and our observations reveal that the target localization diversity is a primary characteristic of lncRNAs in different biotypes. Moreover, we found that lncRNAs in multiple cancers, differentially expressed cancer lncRNAs, and lncRNAs with multiple cancer target proteins are prone to have high target localization diversity. Furthermore, the analysis of gastric cancer helps us to obtain a better understanding that the target localization diversity of lncRNAs is an important feature closely related to clinical prognosis. Overall, we systematically studied the target localization diversity of the lncRNAs and uncovered its association with cancer.

Advanced glycation end products and sorbitol in blood from differently compensated diabetic dogs.

PubMed

Comazzi, S; Bertazzolo, W; Bonfanti, U; Spagnolo, V; Sartorelli, P

2008-06-01

Canine diabetes mellitus (DM) is a common metabolic disorder with long term complications, most of which are caused by glycosylation of structural proteins, decreases in antioxidant concentrations, altered osmotic balance and hypoxia due to impaired oxygen transport. Previous studies have demonstrated that under hyperglycemic conditions canine erythrocytes undergo swelling, probably due to activation of the polyol pathway. The present work aimed to assess the plasma concentration of advanced glycation end (AGE) products, stable Amadori-products generated by non-enzymatic glycosylation of proteins and the intracellular concentration of sorbitol, produced by the activation of polyol pathway in 34 blood samples from diabetic dogs and in 14 controls. AGE products were significantly higher (p<0.01) in plasma from diabetic dogs compared with control animals. The sorbitol concentration in erythrocytes was also significantly higher in diabetic dogs and, in particular, in poorly compensated animals and in dogs with ketonuria. In five cases that were analysed before and after clinical improvement, sorbitol concentration was found to correlate with improvement. These results suggest that non-specific glycosylation is increased and that the polyol pathway is activated in diabetic dogs in a manner that is proportionate to the severity of disease. Moreover, the concentration of AGE products and sorbitol may be useful for monitoring the onset of diabetic complications and assessing the most appropriate therapeutic approaches for management of canine DM.

Holland Code, Job Satisfaction and Productivity in Clothing Factory Workers.

ERIC Educational Resources Information Center

Heesacker, Martin; And Others

Published research on vocational interests and personality has not often assessed the characteristics of workers and the work environment in blue-collar, women-dominated industries. This study administered the Self-Directed Search (Form E) to 318 sewing machine operators in three clothing factories. Holland codes, productivity, job satisfaction,…

Application of Six Sigma/CAP methodology: controlling blood-product utilization and costs.

PubMed

Neri, Robert A; Mason, Cindy E; Demko, Lisa A

2008-01-01

Blood-product components are a limited commodity whose cost is rising. Many patients benefit from their use, but patients who receive transfusions face an unnecessary increased risk for developing infections; fatal, febrile, or allergic reactions; and circulatory overload. To improve patient care, safety, and resource stewardship, transfusion practices must be evaluated for appropriateness (Wilson et al. 2002). A multihospital health system undertook a rigorous study of blood-product utilization patterns and management processes to address cost-control problems in the organization. The system leveraged two process improvement tools widely implemented outside of the healthcare industry: (1) Six Sigma methodology to identify blood-utilization drivers and to standardize transfusion practice, and (2) change acceleration process model to drive effective change. The initiative resulted in a decreased rate of inappropriate transfusions of packed red blood cell from 16 percent to less than 5 percent, improved clinician use of a blood-component order form, establishment of internal benchmarks, enhanced laboratory-to-clinician communication, and better blood-product expense control. The project further demonstrated how out-of-industry tools and methodologies can be adopted, adapted, and systematically applied to generate positive change (Black and Revere 2006).

International codes and agreements to restrict the promotion of harmful products can hold lessons for the control of alcohol marketing.

PubMed

Landon, Jane; Lobstein, Tim; Godfrey, Fiona; Johns, Paula; Brookes, Chris; Jernigan, David

2017-01-01

Background and aims The 2011 UN Summit on Non-Communicable Disease failed to call for global action on alcohol marketing despite calls in the World Health Organization (WHO) Global Action Plan on Non-Communicable Diseases 2013-20 to restrict or ban alcohol advertising. In this paper we ask what it might take to match the global approach to tobacco enshrined in the Framework Convention on Tobacco Control (FCTC), and suggest that public health advocates can learn from the development of the FCTC and the Code of Marketing on infant formula milks and the recent recommendations on restricting food marketing to children. Methods Narrative review of qualitative accounts of the processes that created and monitor existing codes and treaties to restrict the marketing of consumer products, specifically breast milk substitutes, unhealthy foods and tobacco. Findings The development of treaties and codes for market restrictions include: (i) evidence of a public health crisis; (ii) the cost of inaction; (iii) civil society advocacy; (iv) the building of capacity; (v) the management of conflicting interests in policy development; and (vi) the need to consider monitoring and accountability to ensure compliance. Conclusion International public health treaties and codes provide an umbrella under which national governments can strengthen their own legislation, assisted by technical support from international agencies and non-governmental organizations. Three examples of international agreements, those for breast milk substitutes, unhealthy foods and tobacco, can provide lessons for the public health community to make progress on alcohol controls. Lessons include stronger alliances of advocates and health professionals and better tools and capacity to monitor and report current marketing practices and trends. © 2016 Society for the Study of Addiction.

Singer product apertures-A coded aperture system with a fast decoding algorithm

NASA Astrophysics Data System (ADS)

Byard, Kevin; Shutler, Paul M. E.

2017-06-01

A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

The Emerging Roles of Long Non-coding RNA in Cancer.

PubMed

Sanchez Calle, Anna; Kawamura, Yumi; Yamamoto, Yusuke; Takeshita, Fumitaka; Ochiya, Takahiro

2018-05-17

Since comprehensive analysis of the mammalian genome has revealed that the vast majority of genomic products are transcribed in long non-coding RNAs (lncRNAs), increasing attention has been paid towards these transcripts. The applied next-generation sequencing technologies have provided accumulating evidence of dysregulated lncRNAs in cancer. The implication of this finding may be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post-transcriptional processes, aberrant expression of lncRNAs may have repercussions in cell proliferation, tumor progression or metastasis. lncRNAs may act as enhancers, scaffolds or decoys by physically interacting with other RNA species or proteins, resulting in a direct impact on cell signaling cascades. Even though their functional classification is well-established in the context of cancer, clearer characterization in terms of their phenotypic outputs is needed to optimize and identify suitable candidates that enable the development of new therapeutic strategies and the design of novel diagnostic approaches. The present article aims to outline different cancer-associated lncRNAs according to their contribution to tumor suppression or tumor promotion based on their most current functional annotations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Junk DNA and the long non-coding RNA twist in cancer genetics

PubMed Central

Ling, Hui; Vincent, Kimberly; Pichler, Martin; Fodde, Riccardo; Berindan-Neagoe, Ioana; Slack, Frank J.; Calin, George A

2015-01-01

The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions, and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown. Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function, and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer. PMID:25619839

Identification of specific bovine blood biomarkers with a non-targeted approach using HPLC ESI tandem mass spectrometry.

PubMed

Lecrenier, M C; Marbaix, H; Dieu, M; Veys, P; Saegerman, C; Raes, M; Baeten, V

2016-12-15

Animal by-products are valuable protein sources in animal nutrition. Among them are blood products and blood meal, which are used as high-quality material for their beneficial effects on growth and health. Within the framework of the feed ban relaxation, the development of complementary methods in order to refine the identification of processed animal proteins remains challenging. The aim of this study was to identify specific biomarkers that would allow the detection of bovine blood products and processed animal proteins using tandem mass spectrometry. Seventeen biomarkers were identified: nine peptides for bovine plasma powder; seven peptides for bovine haemoglobin powder, including six peptides for bovine blood meal; and one peptide for porcine blood. They were not detected in several commercial compound feed or feed materials, such as blood by-products of other animal origins, milk-derived products and fish meal. These biomarkers could be used for developing a species-specific and blood-specific detection method. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria.

PubMed

Kopf, Matthias; Klähn, Stephan; Scholz, Ingeborg; Hess, Wolfgang R; Voß, Björn

2015-04-22

In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5'UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5'UTR. Such an sRNA/mRNA structure, which we name 'actuaton', represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation.

Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria

PubMed Central

Kopf, Matthias; Klähn, Stephan; Scholz, Ingeborg; Hess, Wolfgang R.; Voß, Björn

2015-01-01

In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5′UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5′UTR. Such an sRNA/mRNA structure, which we name ‘actuaton’, represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation. PMID:25902393

Parametrically defined cerebral blood vessels as non-invasive blood input functions for brain PET studies

NASA Astrophysics Data System (ADS)

Asselin, Marie-Claude; Cunningham, Vincent J.; Amano, Shigeko; Gunn, Roger N.; Nahmias, Claude

2004-03-01

A non-invasive alternative to arterial blood sampling for the generation of a blood input function for brain positron emission tomography (PET) studies is presented. The method aims to extract the dimensions of the blood vessel directly from PET images and to simultaneously correct the radioactivity concentration for partial volume and spillover. This involves simulation of the tomographic imaging process to generate images of different blood vessel and background geometries and selecting the one that best fits, in a least-squares sense, the acquired PET image. A phantom experiment was conducted to validate the method which was then applied to eight subjects injected with 6-[18F]fluoro-L-DOPA and one subject injected with [11C]CO-labelled red blood cells. In the phantom study, the diameter of syringes filled with an 11C solution and inserted into a water-filled cylinder were estimated with an accuracy of half a pixel (1 mm). The radioactivity concentration was recovered to 100 ± 4% in the 8.7 mm diameter syringe, the one that most closely approximated the superior sagittal sinus. In the human studies, the method systematically overestimated the calibre of the superior sagittal sinus by 2-3 mm compared to measurements made in magnetic resonance venograms on the same subjects. Sources of discrepancies related to the anatomy of the blood vessel were found not to be fundamental limitations to the applicability of the method to human subjects. This method has the potential to provide accurate quantification of blood radioactivity concentration from PET images without the need for blood samples, corrections for delay and dispersion, co-registered anatomical images, or manually defined regions of interest.

Towards a complete map of the human long non-coding RNA transcriptome.

PubMed

Uszczynska-Ratajczak, Barbara; Lagarde, Julien; Frankish, Adam; Guigó, Roderic; Johnson, Rory

2018-05-23

Gene maps, or annotations, enable us to navigate the functional landscape of our genome. They are a resource upon which virtually all studies depend, from single-gene to genome-wide scales and from basic molecular biology to medical genetics. Yet present-day annotations suffer from trade-offs between quality and size, with serious but often unappreciated consequences for downstream studies. This is particularly true for long non-coding RNAs (lncRNAs), which are poorly characterized compared to protein-coding genes. Long-read sequencing technologies promise to improve current annotations, paving the way towards a complete annotation of lncRNAs expressed throughout a human lifetime.

40 CFR 80.158 - Product transfer documents (PTDs).

Code of Federal Regulations, 2010 CFR

2010-07-01

... exempt base gasoline to be used for research, development, or test purposes only, the following warning must also be stated on the PTD: “For use in research, development, and test programs only.” (6) The...) Use of product codes and other non-regulatory language. (1) Product codes and other non-regulatory...

Transfusions of blood products and cancer outcomes.

PubMed

Velásquez, J F; Cata, J P

2015-10-01

Approximately half of cancer patients scheduled for major surgery are anemic. Also, a significant number of patients will present to the operating room with low platelet counts and coagulopathic disorders. Unfortunately, administration of red blood cells, platelets concentrates and fresh-frozen plasma is associated with unwanted adverse effects including fever, hemolytic reactions and transfusion-related immunomodulation (TRIM). TRIM is a multifactorial immunologic phenomenon in the recipient mediated by donor leukocytes, microparticles such as ectosomes, and growth factors. As some of these molecules are secreted in a time-dependent manner, blood storage time may play an important in TRIM, although the evidence is limited. Perioperative administration of red blood cells and associated TRIM has also been associated with increased recurrence of certain solid tumors, such as colorectal, lung, and hepatobiliary tumors. In this continuing education article, we review the available evidence on how perioperative blood product transfusions can affect oncological outcomes, such as cancer recurrence. Copyright © 2014 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

Cytokine production by oral and peripheral blood neutrophils in adult periodontitis.

PubMed

Galbraith, G M; Hagan, C; Steed, R B; Sanders, J J; Javed, T

1997-09-01

Proinflammatory cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin 1 beta (IL-1 beta) also possess bone-resorptive properties, and are generally considered to play a role in the pathogenesis of periodontal disease. In the present study, TNF-alpha and IL-1 beta production by oral and peripheral blood polymorphonuclear leukocytes (PMN) was examined in 40 patients with adult periodontitis and 40 orally healthy matched controls. Oral PMN released considerable amounts of both cytokines in unstimulated culture, and there was no difference between patients and controls when the cytokine levels were corrected for cell number. However, when the effect of disease activity was examined, cytokine release by oral PMN was found to be greatest in patients with advanced periodontitis. Within the healthy control group, IL-1 beta production by oral PMN was significantly higher in males (Mann-Whitney test, P = 0.0008). Examination of IL-1 beta production by peripheral blood PMN exposed to recombinant human granulocyte-macrophage colony stimulating factor revealed no difference between the patient and control groups. In contrast, IL-1 beta production by peripheral blood PMN was significantly reduced in patients with advanced disease (Mann-Whitney test, P = 0.02), and peripheral PMN IL-1 beta synthesis was greater in female controls (Mann-Whitney test, P = 0.054). No effect of race on cytokine production could be discerned in patients or controls. These results indicate that several factors influence cytokine production in oral health and disease, and that a dichotomy in cytokine gene expression exists between oral and peripheral blood PMN in adult periodontitis.

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity.

PubMed

Ishikawa, Sohta A; Inagaki, Yuji; Hashimoto, Tetsuo

2012-01-01

In phylogenetic analyses of nucleotide sequences, 'homogeneous' substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, 'RY-coding' and 'non-homogeneous' models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.

Blood Type 0 is not associated with increased blood loss in extensive spine surgery✩

PubMed Central

Komatsu, Ryu; Dalton, Jarrod E.; Ghobrial, Michael; Fu, Alexander Y.; Lee, Jae H.; Egan, Cameron; Sessler, Daniel I.; Kasuya, Yusuke; Turan, Alparslan

2016-01-01

Study Objective To investigate whether Type O blood group status is associated with increased intraoperative blood loss and requirement of blood transfusion in extensive spine surgery. Design Retrospective comparative study. Setting University-affiliated, non-profit teaching hospital. Measurements Data from 1,050 ASA physical status 1, 2, 3, 4, and 5 patients who underwent spine surgeries involving 4 or more vertebral levels were analyzed. Patients with Type O blood were matched to similar patients with other blood types using propensity scores, which were estimated via demographic and morphometric data, medical history variables, and extent of surgery. Intraoperative estimated blood loss (EBL) was compared among matched patients using a linear regression model; intraoperative transfusion requirement in volume of red blood cells, fresh frozen plasma, platelet, cryoprecipitate, cell salvaged blood, volume of intraoperative infusion of hetastarch, 5% albumin, crystalloids, and hospital length of hospital (LOS) were compared using Wilcoxon rank-sum tests. Main Results Intraoperative EBL and requirement of blood product transfusion were similar in patients with Type O blood group and those with other blood groups. Conclusion There was no association between Type O blood and increased intraoperative blood loss or blood transfusion requirement during extensive spine surgery, with similar hospital LOS in Type O and non-O patients. PMID:25172503

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.

PubMed

Lazzarato, F; Franceschinis, G; Botta, M; Cordero, F; Calogero, R A

2004-11-01

RRE allows the extraction of non-coding regions surrounding a coding sequence [i.e. gene upstream region, 5'-untranslated region (5'-UTR), introns, 3'-UTR, downstream region] from annotated genomic datasets available at NCBI. RRE parser and web-based interface are accessible at http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html

Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.

PubMed

Bush, Stephen J; Muriuki, Charity; McCulloch, Mary E B; Farquhar, Iseabail L; Clark, Emily L; Hume, David A

2018-04-24

mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci. Few lncRNAs could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNAs that were assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNAs to identify a consensus set of ruminant lncRNAs and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. In sheep, 20 to 30% of lncRNAs were located close to protein-coding genes with which they are strongly co-expressed, which is consistent with the evolutionary origin of some ncRNAs in enhancer sequences. Nevertheless, most of the lncRNAs are not co-expressed with neighbouring protein-coding genes. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNAs in other species.

Direct detection of falciparum and non-falciparum malaria DNA from a drop of blood with high sensitivity by the dried-LAMP system.

PubMed

Hayashida, Kyoko; Kajino, Kiichi; Simukoko, Humphrey; Simuunza, Martin; Ndebe, Joseph; Chota, Amos; Namangala, Boniface; Sugimoto, Chihiro

2017-01-13

Because of the low sensitivity of conventional rapid diagnostic tests (RDTs) for malaria infections, the actual prevalence of the diseases, especially those caused by non-Plasmodium falciparum (non-Pf) species, in asymptomatic populations remain less defined in countries lacking in well-equipped facilities for accurate diagnoses. Our direct blood dry LAMP system (CZC-LAMP) was applied to the diagnosis of malaria as simple, rapid and highly sensitive method as an alternative for conventional RDTs in malaria endemic areas where laboratory resources are limited. LAMP primer sets for mitochondria DNAs of Plasmodium falciparum (Pf) and human-infective species other than Pf (non-Pf; P. vivax, P. ovale, P. malariae) were designed and tested by using human blood DNA samples from 74 residents from a malaria endemic area in eastern Zambia. These malaria dry-LAMPs were optimized for field or point-of-care operations, and evaluated in the field at a malaria endemic area in Zambia with 96 human blood samples. To determine the sensitivities and specificities, results obtained by the on-site LAMP diagnosis were compared with those by the nested PCR and nucleotide sequencing of its product. The dry LAMPs showed the sensitivities of 89.7% for Pf and 85.7% for non-Pf, and the specificities of 97.2% for Pf and 100% for non-Pf, with purified blood DNA samples. The direct blood LAMP diagnostic methods, in which 1 μl of anticoagulated blood were used as the template, showed the sensitivities of 98.1% for Pf, 92.1% for non-Pf, and the specificities of 98.1% for Pf, 100% for non-Pf. The prevalences of P. falciparum, P. malariae and P. ovale in the surveyed area were 52.4, 25.3 and 10.6%, respectively, indicating high prevalence of asymptomatic carriers in endemic areas in Zambia. We have developed new field-applicable malaria diagnostic tests. The malaria CZC-LAMPs showed high sensitivity and specificity to both P. falciparum and non-P. falciparum. These malaria CZC-LAMPs provide new

Biallelic insertion of a transcriptional terminator via the CRISPR/Cas9 system efficiently silences expression of protein-coding and non-coding RNA genes.

PubMed

Liu, Yangyang; Han, Xiao; Yuan, Junting; Geng, Tuoyu; Chen, Shihao; Hu, Xuming; Cui, Isabelle H; Cui, Hengmi

2017-04-07

The type II bacterial CRISPR/Cas9 system is a simple, convenient, and powerful tool for targeted gene editing. Here, we describe a CRISPR/Cas9-based approach for inserting a poly(A) transcriptional terminator into both alleles of a targeted gene to silence protein-coding and non-protein-coding genes, which often play key roles in gene regulation but are difficult to silence via insertion or deletion of short DNA fragments. The integration of 225 bp of bovine growth hormone poly(A) signals into either the first intron or the first exon or behind the promoter of target genes caused efficient termination of expression of PPP1R12C , NSUN2 (protein-coding genes), and MALAT1 (non-protein-coding gene). Both NeoR and PuroR were used as markers in the selection of clonal cell lines with biallelic integration of a poly(A) signal. Genotyping analysis indicated that the cell lines displayed the desired biallelic silencing after a brief selection period. These combined results indicate that this CRISPR/Cas9-based approach offers an easy, convenient, and efficient novel technique for gene silencing in cell lines, especially for those in which gene integration is difficult because of a low efficiency of homology-directed repair. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Clinical use of indium-111 labeled blood products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loken, M.K.; Clay, M.E.; Carpenter, R.T.

1985-12-01

Following the introduction of In-111 oxine as a label for blood cells by McAffee and Thakur in 1976, these procedures have become increasingly important in the practice of nuclear medicine. Of particular interest are studies involving the use of labeled leukocytes for the detection of focal infection. The clinical utility of labeled platelets is less well developed, although the use of platelets to detect the formation of thrombi in blood vessels and on vascular grafts and prostheses is gaining prominence. This report summarizes the techniques presently employed at the University of Minnesota for the labeling of blood products, and theirmore » clinical use. Consideration also is given to the desired expertise and cost factors involved in the labeling of leukocytes and platelets.43 references.« less

Method and apparatus for non-invasive monitoring of blood glucose

DOEpatents

Thomas, Graham H.; Watson, Roger M.; Noell, J. Oakey

1992-06-09

A new and improved method and apparatus are provided for non-invasive monitoring of changes in blood glucose concentration in a tissue specimen and particularly in an individual. The method uses acoustic velocity measurements for monitoring the effect of glucose concentration upon the density and adiabatic compressibility of the serum. In a preferred embodiment, the acoustic velocity measurements are made through the earlobe of a subject by means of an acoustic probe or monitor which includes a transducer for transmitting and receiving ultrasonic energy pulses to and from the blood flowing in the subject's earlobe and a reflector for facilitating reflection of the acoustic pulses from the blood. The probe is designed in such a way that when properly affixed to an ear, the transducer is positioned flush against the anterior portion of an earlobe while the reflector is positioned flush against the interior portion of the earlobe. A microthermocouple is provided on the probe for monitoring the internal temperature of the blood being sampled. An electrical system, essentially comprising a frequency generator, a time intervalometer and an oscilloscope, is linked to the glucose monitoring probe. The electrical system analyzes selected ones of the pulses reflected from the blood sample in order to determine therefrom the acoustic velocity of the blood which, in turn, provides a representation of the blood glucose concentration levels at the time of the acoustic velocity measurements.

Prevalence of elevated blood pressure in Hispanic versus non-Hispanic 6th graders.

PubMed

Tarlton, Patricia A

2007-02-01

Blood pressure screening was conducted on 4,311 (Hispanic n = 763 [17.7%], White n = 2,566 [59.5%], African American n = 610 [14.1%], Asian n = 136 [3.2%], Multiracial n = 231 [5.4%], and Native American n = 5 [0.1%]) 6th-grade students enrolled in Seminole County, Florida, Public Schools from August to December 2005. Prevalence of obesity was 21% for the overall population, with Hispanics n = 218 (28.6%) having a greater prevalence than non-Hispanics n = 630 (19.0%). Following a second screening, overall prevalence of elevated blood pressure was 1.9%, with Hispanics at 2.6% versus 1.6% for non-Hispanics. This was found to be significant when Hispanics were further compared to the White population. However, when adjusted for obesity, elevated blood pressure was not significant for Hispanics. Results confirm the presence of elevated blood pressure and obesity in all population groups, with an elevated risk for both among the Hispanic population.

Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy

PubMed Central

Miller-Delaney, Suzanne F.C.; Bryan, Kenneth; Das, Sudipto; McKiernan, Ross C.; Bray, Isabella M.; Reynolds, James P.; Gwinn, Ryder; Stallings, Raymond L.

2015-01-01

Temporal lobe epilepsy is associated with large-scale, wide-ranging changes in gene expression in the hippocampus. Epigenetic changes to DNA are attractive mechanisms to explain the sustained hyperexcitability of chronic epilepsy. Here, through methylation analysis of all annotated C-phosphate-G islands and promoter regions in the human genome, we report a pilot study of the methylation profiles of temporal lobe epilepsy with or without hippocampal sclerosis. Furthermore, by comparative analysis of expression and promoter methylation, we identify methylation sensitive non-coding RNA in human temporal lobe epilepsy. A total of 146 protein-coding genes exhibited altered DNA methylation in temporal lobe epilepsy hippocampus (n = 9) when compared to control (n = 5), with 81.5% of the promoters of these genes displaying hypermethylation. Unique methylation profiles were evident in temporal lobe epilepsy with or without hippocampal sclerosis, in addition to a common methylation profile regardless of pathology grade. Gene ontology terms associated with development, neuron remodelling and neuron maturation were over-represented in the methylation profile of Watson Grade 1 samples (mild hippocampal sclerosis). In addition to genes associated with neuronal, neurotransmitter/synaptic transmission and cell death functions, differential hypermethylation of genes associated with transcriptional regulation was evident in temporal lobe epilepsy, but overall few genes previously associated with epilepsy were among the differentially methylated. Finally, a panel of 13, methylation-sensitive microRNA were identified in temporal lobe epilepsy including MIR27A, miR-193a-5p (MIR193A) and miR-876-3p (MIR876), and the differential methylation of long non-coding RNA documented for the first time. The present study therefore reports select, genome-wide DNA methylation changes in human temporal lobe epilepsy that may contribute to the molecular architecture of the epileptic brain. PMID

77 FR 7588 - Blood Products Advisory Committee; Cancellation

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-13

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2012-N-0001] Blood Products Advisory Committee; Cancellation AGENCY: Food and Drug Administration, HHS. ACTION... Research (HFM-71), Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852, Contact 1- 301...

Polarization-multiplexed rate-adaptive non-binary-quasi-cyclic-LDPC-coded multilevel modulation with coherent detection for optical transport networks.

PubMed

Arabaci, Murat; Djordjevic, Ivan B; Saunders, Ross; Marcoccia, Roberto M

2010-02-01

In order to achieve high-speed transmission over optical transport networks (OTNs) and maximize its throughput, we propose using a rate-adaptive polarization-multiplexed coded multilevel modulation with coherent detection based on component non-binary quasi-cyclic (QC) LDPC codes. Compared to prior-art bit-interleaved LDPC-coded modulation (BI-LDPC-CM) scheme, the proposed non-binary LDPC-coded modulation (NB-LDPC-CM) scheme not only reduces latency due to symbol- instead of bit-level processing but also provides either impressive reduction in computational complexity or striking improvements in coding gain depending on the constellation size. As the paper presents, compared to its prior-art binary counterpart, the proposed NB-LDPC-CM scheme addresses the needs of future OTNs, which are achieving the target BER performance and providing maximum possible throughput both over the entire lifetime of the OTN, better.

NPTFit: A Code Package for Non-Poissonian Template Fitting

NASA Astrophysics Data System (ADS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ˜GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

NPTFit: A Code Package for Non-Poissonian Template Fitting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allowmore » for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.« less

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.

PubMed

Zhang, Rui; Deng, Patricia; Jacobson, Dionna; Li, Jin Billy

2017-02-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

PubMed Central

Jacobson, Dionna

2017-01-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3’UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3’UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions. PMID:28166241

Sequence-based heuristics for faster annotation of non-coding RNA families.

PubMed

Weinberg, Zasha; Ruzzo, Walter L

2006-01-01

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

Fragile X mental retardation protein participates in non-coding RNA pathways.

PubMed

Li, En-Hui; Zhao, Xin; Zhang, Ce; Liu, Wei

2018-02-20

Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells. Subsequent studies showed that the Drosophila FMRP participates in piRNA pathway by interacting with Aub, Ago1 and Piwi in the maintenance of normal chromatin structures and genomic stability. More recent studies showed that FMRP is associated with lncRNA pathway, suggesting a potential role for the involvement in the clinical manifestations. In this review, we summarize the novel findings and explore the relationship between FMRP and non-coding RNA pathways, particularly the piRNA pathway, thereby providing critical insights on the molecular pathogenesis of Fragile X syndrome, and potential translational applications in clinical management of the disease.

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

PubMed Central

Holdt, Lesca M.; Stahringer, Anika; Sass, Kristina; Pichler, Garwin; Kulak, Nils A.; Wilfert, Wolfgang; Kohlmaier, Alexander; Herbst, Andreas; Northoff, Bernd H.; Nicolaou, Alexandros; Gäbel, Gabor; Beutner, Frank; Scholz, Markus; Thiery, Joachim; Musunuru, Kiran; Krohn, Knut; Mann, Matthias; Teupser, Daniel

2016-01-01

Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. Here we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers atheroprotection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. CircANRIL binds to pescadillo homologue 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis in vascular smooth muscle cells and macrophages. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key cell functions in atherosclerosis. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring atheroprotection, thereby showing that circularization of long non-coding RNAs may alter RNA function and protect from human disease. PMID:27539542

Continuous non-invasive blood glucose monitoring by spectral image differencing method

NASA Astrophysics Data System (ADS)

Huang, Hao; Liao, Ningfang; Cheng, Haobo; Liang, Jing

2018-01-01

Currently, the use of implantable enzyme electrode sensor is the main method for continuous blood glucose monitoring. But the effect of electrochemical reactions and the significant drift caused by bioelectricity in body will reduce the accuracy of the glucose measurements. So the enzyme-based glucose sensors need to be calibrated several times each day by the finger-prick blood corrections. This increases the patient's pain. In this paper, we proposed a method for continuous Non-invasive blood glucose monitoring by spectral image differencing method in the near infrared band. The method uses a high-precision CCD detector to switch the filter in a very short period of time, obtains the spectral images. And then by using the morphological method to obtain the spectral image differences, the dynamic change of blood sugar is reflected in the image difference data. Through the experiment proved that this method can be used to monitor blood glucose dynamically to a certain extent.

"I intend to donate but ...": non-donors' views of blood donation in the UK.

PubMed

McVittie, Chris; Harris, Lisa; Tiliopoulos, Niko

2006-02-01

Although only 6% of the eligible United Kingdom population regularly donate blood, reasons for low donation rates remain poorly understood. In a grounded theory investigation, blood donors (n = 23) and non-donors (n = 27) completed a questionnaire that included 15 open-ended items. Semi-structured interviews were conducted with sub-samples of donors (n = 5) and non-donors (n = 7). Analysis of open-ended responses and interview transcripts identified five themes. Three themes, namely pro-social views, helping behaviour and awareness had similar relevance for donors and non-donors. Two themes, anxiety and practical difficulties, were used by non-donors to account for non-donation despite intentions to donate. Although non-donors' anxieties may be difficult to overcome, perceived practical difficulties provide scope for intervention. The removal of perceived barriers to donation offers one way of increasing donation rates.

Characteristics and Outcomes of Blood Product Transfusion During Critical Care Transport.

PubMed

Mena-Munoz, Jorge; Srivastava, Udayan; Martin-Gill, Christian; Suffoletto, Brian; Callaway, Clifton W; Guyette, Francis X

2016-01-01

Civilian out-of-hospital transfusions have not been adequately studied. This study seeks to characterize patients receiving out-of-hospital blood product transfusion during critical care transport. We studied patients transported by a regional critical care air-medical service who received blood products during transport. This service carries two units of uncrossmatched packed Red Blood Cells (pRBCs) on every transport in addition to blood obtained from referring facilities. The pRBC are administered according to a protocol for the treatment of hemorrhagic shock or based on medical command physician order. Transfusion amount was categorized into three groups based on the volume transfused (<350 mL, 350-700 mL, >700 mL). The association between prehospital transfusion and in-hospital outcomes (mortality, subsequent blood transfusion and emergent surgery) was estimated using logistic regression models, controlling for age, first systolic blood pressure, first heart rate, Glasgow Coma Score, time of transfer, and length of hospital admission. Among the 1,440 critical care transports with transfusions examined, 81% were for medical patients, being gastrointestinal hemorrhage the most common indication (26%, CI 24-28%). pRBC transfusions were associated with emergent surgery (OR = 1.81, 95% CI = 1.31-2.52) and in-hospital transfusions (OR = 2.00, 95% CI = 1.46-2.76). Those with transfusions >700 mL were associated with emergent surgery (OR = 1.79, 95% CI = 1.10-2.92) and mortality (OR = 2.11; 95% CI = 1.21-3.69). In this sample, the majority of patients receiving blood products during air-medical transport were transfused for medic conditions; gastrointestinal hemorrhage was the most common chief complaint. The pRBC transfusions were associated with emergent surgery and in-hospital transfusion. Transfusions of >700 mL were associated with mortality.

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

PubMed Central

Rose, Dominic; Stadler, Peter F.

2011-01-01

Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element. PMID:22303364

21 CFR 607.7 - Establishment registration and product listing of blood banks and other firms manufacturing human...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Establishment registration and product listing of blood banks and other firms manufacturing human blood and blood products. 607.7 Section 607.7 Food and... manufacturing of blood products are required to register, pursuant to section 510 of the Federal Food, Drug, and...

21 CFR 607.7 - Establishment registration and product listing of blood banks and other firms manufacturing human...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Establishment registration and product listing of blood banks and other firms manufacturing human blood and blood products. 607.7 Section 607.7 Food and... manufacturing of blood products are required to register, pursuant to section 510 of the Federal Food, Drug, and...

Studies on the mechanism of endogenous pyrogen production. II. Role of cell products in the regulation of pyrogen release from blood leukocytes.

PubMed

Bodel, P

1974-09-01

Some characteristics of the process by which endogenous pyrogen (EP), the mediator of fever, is released from cells were examined by using human blood leukocytes incubated in vitro. Studies were designed to examine a possible role for leukocyte products, including EP, in the induction, augmentation, or suppression of pyrogen release by blood leukocytes. Products of stimulated leukocytes, including a partially purified preparation of EP, did not induce significant activation of nonstimulated cells. Also, no evidence was obtained that stimulated cell products either augment or inhibit pyrogen production by other stimulated cells. A feedback control of EP production was thus not observed. A crude preparation of EP, containing other products of activated cells, maintained its pyrogenicity when incubated at pH 7.4 but not at pH 5.0. These studies thus provide no support for hypothesized control mechanisms regulating production of EP by blood leukocytes. By contrast, local inactivation of EP at inflammatory sites may modify the amount of EP entering the blood, and hence fever.